Antibody that binds zinc transporter protein 108P5H8

ABSTRACT

A novel gene (designated 108P5H8) and its encoded protein, and variants thereof, are described wherein 108P5H8 exhibits tissue specific expression in normal adult tissue, and is aberrantly expressed in the cancers listed in Table I. Consequently, 108P5H8 provides a diagnostic, prognostic, prophylactic and/or therapeutic target for cancer. The 108P5H8 gene or fragment thereof, or its encoded protein, or variants thereof, or a fragment thereof, can be used to elicit a humoral or cellular immune response; antibodies or T cells reactive with 191P1E1B can be used in active or passive immunization.

RELATED APPLICATIONS

This application claims priority from provisional application U.S. Ser. No 60/256,210 filed 15 Dec. 2000, the contents of which are incorporated herein by reference.

SUBMISSION ON COMPACT DISC

The contents of the following submission on compact discs are incorporated herein by reference in its entirety: A compact disc copy of the Sequence Listing (COPY 1) (file name: 511582002500, date recorded: 2 Jun. 2002, size: 434 KB); a duplicate compact disc copy of Sequence Listing (COPY 2) (file name: 511582002500, date recorded: 2 Jun. 2002, size: 434 KB); a computer readable form copy of the Sequence Listing (CRF COPY) (file name: 511582002500, date recorded: 2 Jun. 2002, size: 434 KB).

FIELD OF THE INVENTION

The invention described herein relates to a gene and its encoded protein, termed 108P5H8, expressed in certain cancers such as those listed in Table I, and to diagnostic, prognostic, prophylactic and/or therapeutic methods and compositions useful in the management of cancers that express 108P5H8.

BACKGROUND OF THE INVENTION

Cancer is the second leading cause of human death next to coronary disease. Worldwide, millions of people die from cancer every year. In the United States alone, as reported by the American Cancer Society, cancer causes the death of well over a half-million people annually, with over 1.2 million new cases diagnosed per year. While deaths from heart disease have been declining significantly, those resulting from cancer generally are on the rise. In the early part of the next century, cancer is predicted to become the leading cause of death.

Worldwide, several cancers stand out as the leading killers. In particular, carcinomas of the lung, prostate, breast, colon, pancreas, and ovary represent the primary causes of cancer death. These and virtually all other carcinomas share a common lethal feature. With very few exceptions, metastatic disease from a carcinoma is fatal. Moreover, even for those cancer patients who initially survive their primary cancers, common experience has shown that their lives are dramatically altered. Many cancer patients experience strong anxieties driven by the awareness of the potential for recurrence or treatment failure. Many cancer patients experience physical debilitations following treatment. Furthermore, many cancer patients experience a recurrence.

Worldwide, prostate cancer is the fourth most prevalent cancer in men. In North America and Northern Europe, it is by far the most common cancer in males and is the second leading cause of cancer death in men. In the United States alone, well over 30,000 men die annually of this disease—second only to lung cancer. Despite the magnitude of these figures, there is still no effective treatment for metastatic prostate cancer. Surgical prostatectomy, radiation therapy, hormone ablation therapy, surgical castration and chemotherapy continue to be the main treatment modalities. Unfortunately, these treatments are ineffective for many and are often associated with undesirable consequences.

On the diagnostic front, the lack of a prostate tumor marker that can accurately detect early-stage, localized tumors remains a significant limitation in the diagnosis and management of this disease. Although the serum prostate specific antigen (PSA) assay has been a very useful tool, however its specificity and general utility is widely regarded as lacking in several important respects.

Progress in identifying additional specific markers for prostate cancer has been improved by the generation of prostate cancer xenografts that can recapitulate different stages of the disease in mice. The LAPC (Los Angeles Prostate Cancer) xenografts are prostate cancer xenografts that have survived passage in severe combined immune deficient (SCID) mice and have exhibited the capacity to mimic the transition from androgen dependence to androgen independence (Klein et al., 1997, Nat. Med. 3:402). More recently identified prostate cancer markers include PCTA-1 (Su et al., 1996, Proc. Natl. Acad. Sci. USA 93: 7252), prostate-specific membrane (PSM) antigen (Pinto et al., Clin Cancer Res 1996 September 2 (9): 1445-51), STEAP (Hubert, et al., Proc Natl Acad Sci USA. 1999 Dec. 7; 96(25): 14523-8) and prostate stem cell antigen (PSCA) (Reiter et al., 1998, Proc. Natl. Acad. Sci. USA 95: 1735).

While previously identified markers such as PSA, PSM, PCTA and PSCA have facilitated efforts to diagnose and treat prostate cancer, there is need for the identification of additional markers and therapeutic targets for prostate and related cancers in order to further improve diagnosis and therapy.

Renal cell carcinoma (RCC) accounts for approximately 3 percent of adult malignancies. Once adenomas reach a diameter of 2 to 3 cm, malignant potential exists. In the adult, the two principal malignant renal tumors are renal cell adenocarcinoma and transitional cell carcinoma of the renal pelvis or ureter. The incidence of renal cell adenocarcinoma is estimated at more than 29,000 cases in the United States, and more than 11,600 patients died of this disease in 1998. Transitional cell carcinoma is less frequent, with an incidence of approximately 500 cases per year in the United States.

Surgery has been the primary therapy for renal cell adenocarcinoma for many decades. Until recently, metastatic disease has been refractory to any systemic therapy. With recent developments in systemic therapies, particularly immunotherapies, metastatic renal cell carcinoma may be approached aggressively in appropriate patients with a possibility of durable responses. Nevertheless, there is a remaining need for effective therapies for these patients.

Of all new cases of cancer in the United States, bladder cancer represents approximately 5 percent in men (fifth most common neoplasm) and 3 percent in women (eighth most common neoplasm). The incidence is increasing slowly, concurrent with an increasing older population. In 1998, there was an estimated 54,500 cases, including 39,500 in men and 15,000 in women. The age-adjusted incidence in the United States is 32 per 100,000 for men and 8 per 100,000 in women. The historic male/female ratio of 3:1 may be decreasing related to smoking patterns in women. There were an estimated 11,000 deaths from bladder cancer in 1998 (7,800 in men and 3,900 in women). Bladder cancer incidence and mortality strongly increase with age and will be an increasing problem as the population becomes more elderly.

Most bladder cancers recur in the bladder. Bladder cancer is managed with a combination of transurethral resection of the bladder (TUR) and intravesical chemotherapy or immunotherapy. The multifocal and recurrent nature of bladder cancer points out the limitations of TUR. Most muscle-invasive cancers are not cured by TUR alone. Radical cystectomy and urinary diversion is the most effective means to eliminate the cancer but carry an undeniable impact on urinary and sexual function. There continues to be a significant need for treatment modalities that are beneficial for bladder cancer patients.

An estimated 130,200 cases of colorectal cancer occurred in 2000 in the United States, including 93,800 cases of colon cancer and 36,400 of rectal cancer. Colorectal cancers are the third most common cancers in men and women. Incidence rates declined significantly during 1992-1996 (−2.1% per year).

Research suggests that these declines have been due to increased screening and polyp removal, preventing progression of polyps to invasive cancers. There were an estimated 56,300 deaths (47,700 from colon cancer, 8,600 from rectal cancer) in 2000, accounting for about 11% of all U.S. cancer deaths.

At present, surgery is the most common form of therapy for colorectal cancer, and for cancers that have not spread, it is frequently curative. Chemotherapy, or chemotherapy plus radiation, is given before or after surgery to most patients whose cancer has deeply perforated the bowel wall or has spread to the lymph nodes. A permanent colostomy (creation of an abdominal opening for elimination of body wastes) is occasionally needed for colon cancer and is infrequently required for rectal cancer. There continues to be a need for effective diagnostic and treatment modalities for colorectal cancer.

There were an estimated 164,100 new cases of lung and bronchial cancer in 2000, accounting for 14% of all U.S. cancer diagnoses. The incidence rate of lung and bronchial cancer is declining significantly in men, from a high of 86.5 per 100,000 in 1984 to 70.0 in 1996. In the 1990s, the rate of increase among women began to slow. In 1996, the incidence rate in women was 42.3 per 100,000.

Lung and bronchial cancer caused an estimated 156,900 deaths in 2000, accounting for 28% of all cancer deaths. During 1992-1996, mortality from lung cancer declined significantly among men (−1.7% per year) while rates for women were still significantly increasing (0.9% per year). Since 1987, more women have died each year of lung cancer than breast cancer, which, for over 40 years, was the major cause of cancer death in women. Decreasing lung cancer incidence and mortality rates most likely resulted from decreased smoking rates over the previous 30 years; however, decreasing smoking patterns among women lag behind those of men. Of concern, although the declines in adult tobacco use have slowed, tobacco use in youth is increasing again.

Treatment options for lung and bronchial cancer are determined by the type and stage of the cancer and include surgery, radiation therapy, and chemotherapy. For many localized cancers, surgery is usually the treatment of choice. Because the disease has usually spread by the time it is discovered, radiation therapy and chemotherapy are often needed in combination with surgery. Chemotherapy alone or combined with radiation is the treatment of choice for small cell lung cancer; on this regimen, a large percentage of patients experience remission, which in some cases is long lasting. There is however, an ongoing need for effective treatment and diagnostic approaches for lung and bronchial cancers.

An estimated 182,800 new invasive cases of breast cancer were expected to occur among women in the United States during 2000. Additionally, about 1,400 new cases of breast cancer were expected to be diagnosed in men in 2000. After increasing about 4% per year in the 1980s, breast cancer incidence rates in women have leveled off in the 1990s to about 110.6 cases per 100,000.

In the U.S. alone, there were an estimated 41,200 deaths (40,800 women, 400 men) in 2000 due to breast cancer. Breast cancer ranks second among cancer deaths in women. According to the most recent data, mortality rates declined significantly during 1992-1996 with the largest decreases in younger women, both white and black. These decreases were probably the result of earlier detection and improved treatment.

Taking into account the medical circumstances and the patient's preferences, treatment of breast cancer may involve lumpectomy (local removal of the tumor) and removal of the lymph nodes under the arm; mastectomy (surgical removal of the breast) and removal of the lymph nodes under the arm; radiation therapy; chemotherapy; or hormone therapy. Often, two or more methods are used in combination. Numerous studies have shown that, for early stage disease, long-term survival rates after lumpectomy plus radiotherapy are similar to survival rates after modified radical mastectomy. Significant advances in reconstruction techniques provide several options for breast reconstruction after mastectomy. Recently, such reconstruction has been done at the same time as the mastectomy.

Local excision of ductal carcinoma in situ (DCIS) with adequate amounts of surrounding normal breast tissue may prevent the local recurrence of the DCIS. Radiation to the breast and/or tamoxifen may reduce the chance of DCIS occurring in the remaining breast tissue. This is important because DCIS, if left untreated, may develop into invasive breast cancer. Nevertheless, there are serious side effects or sequelae to these treatments. There is, therefore, a need for efficacious breast cancer treatments.

There were an estimated 23,100 new cases of ovarian cancer in the United States in 2000. It accounts for 4% of all cancers among women and ranks second among gynecologic cancers. During 1992-1996, ovarian cancer incidence rates were significantly declining. Consequent to ovarian cancer, there were an estimated 14,000 deaths in 2000. Ovarian cancer causes more deaths than any other cancer of the female reproductive system.

Surgery, radiation therapy, and chemotherapy are treatment options for ovarian cancer. Surgery usually includes the removal of one or both ovaries, the fallopian tubes (salpingo-oophorectomy), and the uterus (hysterectomy). In some very early tumors, only the involved ovary will be removed, especially in young women who wish to have children. In advanced disease, an attempt is made to remove all intra-abdominal disease to enhance the effect of chemotherapy. There continues to be an important need for effective treatment options for ovarian cancer.

There were an estimated 28,300 new cases of pancreatic cancer in the United States in 2000. Over the past 20 years, rates of pancreatic cancer have declined in men. Rates among women have remained approximately constant but may be beginning to decline. Pancreatic cancer caused an estimated 28,200 deaths in 2000 in the United States. Over the past 20 years, there has been a slight but significant decrease in mortality rates among men (about −0.9% per year) while rates have increased slightly among women.

Surgery, radiation therapy, and chemotherapy are treatment options for pancreatic cancer. These treatment options can extend survival and/or relieve symptoms in many patients but are not likely to produce a cure for most. There is a significant need for additional therapeutic and diagnostic options for pancreatic cancer.

SUMMARY OF THE INVENTION

The present invention relates to a gene, designated 108P5H8, that has now been found to be over-expressed in the cancer(s) listed in Table I. Northern blot expression analysis of 108P5H8 gene expression in normal tissues shows a restricted expression pattern in adult tissues. The nucleotide (FIG. 2) and amino acid (FIG. 2, and FIG. 3) sequences of 108P5H8 are provided. The tissue-related profile of 108P5H8 in normal adult tissues, combined with the over-expression observed in the tumors listed in Table I, shows that 108P5H8 is aberrantly over-expressed in at least some cancers, and thus serves as a useful diagnostic, prophylactic, prognostic, and/or therapeutic target for cancers of the tissue(s) such as those listed in Table I.

The invention provides polynucleotides corresponding or complementary to all or part of the 108P5H8 genes, mRNAs, and/or coding sequences, preferably in isolated form, including polynucleotides encoding 108P5H8-related proteins and fragments of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25 contiguous amino acids; at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100 or more than 100 contiguous amino acids of a 108P5H8-related protein, as well as the peptides/proteins themselves; DNA, RNA, DNA/RNA hybrids, and related molecules, polynucleotides or oligonucleotides complementary or having at least a 90% homology to the 108P5H8 genes or mRNA sequences or parts thereof, and polynucleotides or oligonucleotides that hybridize to the 108P5H8 genes, mRNAs, or to 108P5H8-encoding polynucleotides. Also provided are means for isolating cDNAs and the genes encoding 108P5H8. Recombinant DNA molecules containing 108P5H8 polynucleotides, cells transformed or transduced with such molecules, and host-vector systems for the expression of 108P5H8 gene products are also provided. The invention further provides antibodies that bind to 108P5H8 proteins and polypeptide fragments thereof, including polyclonal and monoclonal antibodies, murine and other mammalian antibodies, chimeric antibodies, humanized and fully human antibodies, and antibodies labeled with a detectable marker or therapeutic agent. In certain embodiments there is a proviso that the entire nucleic acid sequence of FIG. 2 is not encoded and/or the entire amino acid sequence of FIG. 2 is not prepared. In certain embodiments, the entire nucleic acid sequence of FIG. 2 is encoded and/or the entire amino acid sequence of FIG. 2 is prepared, either of which are in respective human unit dose forms.

The invention further provides methods for detecting the presence and status of 108P5H8 polynucleotides and proteins in various biological samples, as well as methods for identifying cells that express 108P5H8. A typical embodiment of this invention provides methods for monitoring 108P5H8 gene products in a tissue or hematology sample having or suspected of having some form of growth dysregulation such as cancer.

The invention further provides various immunogenic or therapeutic compositions and strategies for treating cancers that express 108P5H8 such as cancers of tissues listed in Table I, including therapies aimed at inhibiting the transcription, translation, processing or function of 108P5H8 as well as cancer vaccines. In one aspect, the invention provides compositions, and methods comprising them, for treating a cancer that expresses 108P5H8 in a human subject wherein the composition comprises a carrier suitable for human use and a human unit dose of one or more than one agent that inhibits the production or function of 108P5H8. Preferably, the carrier is a uniquely human carrier. In another aspect of the invention, the agent is a moiety that is immunoreactive with 108P5H8 protein. Non-limiting examples of such moieties include, but are not limited to, antibodies (such as single chain, monoclonal, polyclonal, humanized, chimeric, or human antibodies), functional equivalents thereof (whether naturally occurring or synthetic), and combinations thereof. The antibodies can be conjugated to a diagnostic or therapeutic moiety. In another aspect, the agent is a small molecule as defined herein.

In another aspect, the agent comprises one or more than one peptide which comprises a cytotoxic T lymphocyte (CTL) epitope that binds an HLA class I molecule in a human to elicit a CTL response to 108P5H8 and/or one or more than one peptide which comprises a helper T lymphocyte (HTL) epitope which binds an HLA class II molecule in a human to elicit an HTL response. The peptides of the invention may be on the same or on one or more separate polypeptide molecules. In a further aspect of the invention, the agent comprises one or more than one nucleic acid molecule that expresses one or more than one of the CTL or HTL response stimulating peptides as described above. In yet another aspect of the invention, the one or more than one nucleic acid molecule may express a moiety that is immunologically reactive with 108P5H8 as described above. The one or more than one nucleic acid molecule may also be, or encodes, a molecule that inhibits production of 108P5H8. Non-limiting examples of such molecules include, but are not limited to, those complementary to a nucleotide sequence essential for production of 108P5H8 (e.g. antisense sequences or molecules that form a triple helix with a nucleotide double helix essential for 108P5H8 production) or a ribozyme effective to lyse 108P5H8 mRNA.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. The 108P5H8 sequence of 448 nucleotides (SEQ ID NO: 2568).

FIG. 2. The cDNA (SEQ ID. NO. : 2569) and amino acid sequence (SEQ ID. NO. : 2570) of 108P5H8 v.1 is shown in FIG. 2A. The start methionine is underlined. The open reading frame extends from nucleic acid 253-1542 including the stop codon. The nucleic acid (SEQ ID. NO. : 2571) and amino acid sequence of 108P5H8 variant 2 (SEQ ID. NO. : 2572) is shown in FIG. 2B, the codon for the start methionine is underlined. The open reading frame for variant 2 extends from nucleic acid 1 to 1290 including the stop codon. The nucleic acid (SEQ ID. NO.: 2573) and amino acid sequence of 108P5F18 variant 3 (SEQ ID. NO. : 2574) is shown in FIG. 2C, the codon for the start methionine is underlined. The open reading frame for variant 3 extends from nucleic acid 1-1290 including the stop codon.

FIG. 3. Amino acid sequence of 108P5H8 variant 1 and of 108P5H8 variant 2 (SEQ ID. NO. : 2572) is shown in FIG. 3A. The proteins encoded by the variant 1 and variant 2 nucleic acid sequences are identical and each have 429 amino acids. The amino acid sequence of 1 08P5H8 variant 3 (SEQ ID. NO. : 2574) is shown in FIG. 3B, the 108P5H8 v.3 protein has 429 amino acids.

FIG. 4. 4A shows nucleotide sequence alignments of 108P5H8 variants 1-3 and 4B shows amino acid alignments of 108P5H8 variant 1 (SEQ ID. NO. : 2570), variant 2 (SEQ ID. NO. : 2572) and variant 3 (SEQ ID. NO. : 2574).

FIG. 5. Hydrophilicity amino acid profile of 108P5H8 determined by computer algorithm sequence analysis using the method of Hopp and Woods (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828) accessed on the Protscale website through the ExPasy molecular biology server.

FIG. 6. Hydropathicity amino acid profile of 108P5H8 determined by computer algorithm sequence analysis using the method of Kyte and Doolittle (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105-132) accessed on the ProtScale website through the ExPasy molecular biology server.

FIG. 7. Percent accessible residues amino acid profile of 108P5H8 determined by computer algorithm sequence analysis using the method of Janin (Janin J., 1979 Nature 277:491-492) accessed on the ProtScale website through the ExPasy molecular biology server.

FIG. 8. Average flexibility amino acid profile of 108P5H8 determined by computer algorithm sequence analysis using the method of Bhaskaran and Ponnuswamy (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242-255) accessed on the ProtScale website through the ExPasy molecular biology server.

FIG. 9. Beta-turn amino acid profile of 108P5H8 determined by computer algorithm sequence analysis using the method of Deleage and Roux (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294) accessed on the ProtScale website through the ExPasy molecular biology server.

FIG. 10. Expression of 108P5H8 by RT-PCR. First strand cDNA was prepared from vital pool 1 (VP1: liver, lung and kidney), vital pool 2 (VP2, pancreas, colon and stomach), prostate xenograft pool (LAPC-4AD, LAPC-4AI, LAPC-9AD, LAPC-9AI), normal thymus, prostate cancer pool, bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, ovary cancer pool, breast cancer pool, metastasis cancer pool, pancreas cancer pool, and from prostate cancer metastasis to lymph node from 2 different patients. Normalization was performed by PCR using primers to actin and GAPDH. Semi-quantitative PCR using primers to 108P5H8 was performed at 26 and 30 cycles of amplification. Strong expression of 108P5H8 was observed in prostate cancer xenograft pool, prostate cancer pool and in the 2 different prostate cancer metastasis samples. Lower expression was detected in bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, ovary cancer pool, breast cancer pool, metastasis pool, pancreas cancer pool, VP1 and VP2.

FIG. 11. Expression of 108P5H8 in normal human tissues and in prostate cancer xenografts. (A and B) Two multiple tissue Northern blots, with 2 mg of mRNA/lane, were probed with 108P5H8 sequence. Size standards in kilobases (kb) are indicated on the side. The results show strong expression of an approximately 7 kb 108P5H8 transcript in prostate and lower expression in other tissues. (C) RNA was extracted from normal prostate, and from prostate cancer xenografts, LAPC-4AD, LAPC-4AI, LAPC-9AD, and LAPC-9AI. Northern blot with 10 mg of total RNA/lane was probed with 108P5H8 sequence. Size standards in kilobases (kb) are indicated on the side. The results show expression of 108P5H8 in all 4 xenografts and in normal prostate.

FIG. 12. Expression of 108P5H8 in prostate cancer xenografts. RNA was extracted from prostate cancer xenografts, LAPC-4AD, and LAPC-9AD, injected either subcutaneously (sc) or intratibially (it) within the mouse bone. LAPC-4 was also grown within a human bone implant in SCID mice (LAPC-4 AD²). Northern blots with 10 μg of total RNA/lane were probed with the 108P5H8 SSH fragment. Size standards in kilobases (kb) are indicated on the side. Results show expression of 108P5H8 in all prostate cancer xenograft tissues tested.

FIG. 13. Expression of 108P5H8 in human cancer cell lines. RNA was extracted from a panel of human cancer cell lines. Northern blots with 10 mg of total RNA/lane were probed with the 108P5H8 SSH fragment. Size standards in kilobases (kb) are indicated on the side. Results show that 108P5H8 is expressed in all cell lines tested such as prostate, bladder, brain, lung, kidney, breast, testis and ovary cancer cell lines.

FIG. 14. Expression of 108P5H8 in patient cancer specimens and cancer cell lines. Expression of 108P5H8 was assayed in a panel of human cancers (T) and their respective matched normal tissues (N) on RNA dot blots. 108P5H8 expression was seen in prostate, kidney, uterus and stomach cancers. The expression detected in some normal adjacent tissues (isolated from diseased tissues), but not in normal tissues (isolated from healthy donors), may indicate that these tissues are not fully normal and that 108P5H8 may be expressed in early-stage tumors. 108P5H8 was also expressed in all 9 human cancer cell lines tested.

FIG. 15. Expression of 108P5H8 in prostate cancer patient specimens. RNA was extracted from prostate tumors (T) and matched normal adjacent tissue (N_(AT)) isolated from prostate cancer patients. Northern blots with 10 mg of total RNA/lane were probed with 108P5H8 sequence. Size standards in kilobases (kb) are indicated on the side. The results show expression of 108P5H8 in the two prostate tumors and in the normal matched tissues.

FIG. 16. 108P5H8 is not Androgen-Regulated. LNCaP cells were grown in charcoal-stripped medium and stimulated with the synthetic androgen mibolerone, for either 14 or 24 hours. Northern blots with 10 mg of total RNA/lane were probed with either the 108P5H8 sequence (A), or with the androgen-regulated gene PSA (B). A picture of the ethidium-bromide staining of the RNA gel is also presented (C). Results show expression of 108P5H8 is not regulated by androgen. The experimental samples were confirmed by testing for the expression of the androgen-regulated prostate cancer gene PSA (B). This experiment shows that, as expected, PSA levels go down in presence of charcoal-stripped serum, and expression is induced at 14 and 24 hours in presence of the synthetic androgen.

FIG. 17. Expression of 108P5H8 in cancer metastasis patient specimens. RNA was extracted from prostate cancer metastasis to lymph node obtained from two different patient, as well as from normal bladder (NB), normal kidney (NK), normal lung (NL), normal breast (NBr), normal ovary (NO), and normal pancreas (NPa). Northern blots with 10 mg of total RNA/lane were probed with 108P5H8 sequence. Size standards in kilobases (kb) are indicated on the side. The results show expression of 108P5H8 in both cancer metastasis samples but not in normal tissues.

FIG. 18. Secondary structure and transmembrane prediction for 108P5H8 (SEQ ID. NO. : 2570). The secondary structure of 108P5H8 protein was predicted using the HNN—Hierarchical Neural Network method (Guermeur, 1997), accessed from the ExPasy molecular biology server. This method predicts the presence and location of alpha helices, extended strands, and random coils from the primary protein sequence. The percent of the protein in a given secondary structure is also given.

FIG. 19. Transmembrane prediction for 108P5H8. A. Schematic representation of the probability of existence of transmembrane regions and orientation of 108P5H8 based on the TMpred algorithm of Hofmann and Stoffel which utilizes TMBASE (K. Hofmann, W. Stoffel. TMBASE—A database of membrane spanning protein segments Biol. Chem. Hoppe-Seyler 374:166, 1993). B. Schematic representation of the probability of the existence of transmembrane regions and the extracellular and intracellular orientation of 108P5H8 based on the TMHMM algorithm of Sonnhammer, von Heijne, and Krogh (Erik L. L. Sonnhammer, Gunnar von Heijne, and Anders Krogh: A hidden Markov model for predicting transmembrane helices in protein sequences. In Proc. of Sixth Int. Conf. on Intelligent Systems for Molecular Biology, p 175-182 Ed J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen Menlo Park, CA: AAAI Press, 1998). The TMpred and TMHMM algorithms are accessed from the ExPasy molecular biology server. The results of the transmembrane prediction programs presented in A and B depict 108P5H8 as containing 6 transmembrane domains.

FIG. 20. Androgen-independent expression of 108P5H8 in prostate cancer cells. Western analysis of the indicated cell lysates were carried out with a 1:2000 dilution of an anti-108P5H8 polyclonal antibody derived from immunization of a rabbit with a GST-fusion protein encoding amino acids 1-112 of 108P5H8. 108P5H8 specific bands were developed by incubation with an anti-rabbit HRP-conjugated secondary antibody and visualized by enhanced chemiluminescence and exposure to autoradiography film. Indicated with an arrow is the full length 108P5H8 protein. 293T cells overexpressing Myc His-tagged 108P5H8 serves as a positive control

FIG. 21. Surface expression of 108P5H8 in prostate cancer cells. LNCaP and LAPC4 cells were subjected to flow cytometric and fluorescence microscopic analysis of 108P5H8 expression using an anti-108P5H8 polyclonal antibody or control rabbit IgG. Fluorescence was monitored following incubation with an FITC-conjugated anti-rabbit IgG secondary antibody

FIG. 22. Surface expression of 108P5H8 in 293T cells. 293T cells were transfected with either empty control vector or with pCDNA 3.1 encoding the 108P5H8 cDNA and subjected to flow cytometry and fluorescence microscopy using an anti-108P5H8 polyclonal antibody (1:100 dilution). Fluorescence was monitored following incubation with an FITC-conjugated anti-rabbit IgG secondary antibody. 293T-108P5H8 cells exhibited strong surface fluorescence.

FIG. 23. Expression of 108P5H8 in prostate and ovarian cancer patient specimens. Lysates from tumor (PCa) and normal adjacent tissue (NAT) from 2 prostate cancer patients and from a prostate cancer metastasis and tumor and normal adjacent tissue from an ovarian cancer patient were subjected to Western analysis using anti-108P5H8 polyclonal antibody as described in FIG. 20. Indicated with an arrow is a 48 kD band representing full length 1-08P5H8. 108P5H8 protein was present in the tumor tissue from the 2 prostate cancer patients and the metastasis sample and in the normal adjacent tissue of 1 of the patients. 108P5H8 was also expressed in the ovarian cancer sample but not in normal ovary. Low expression is seen in RNA positive 293T cells and strong expression in the overexpressed 293T-108P5H8 cells.

FIG. 24. Expression of 108P5H8 in engineered cell lines. PC3 human prostate cancer cells and NIH3T3 murine fibroblasts were engineered to stably express 108P5H8 through infection with retrovirus harboring the 108P5H8 cDNA. Stable lines were generated by G418 selection for neomycin resistance. 108P5H8 expression was verified by Western blot analysis with anti-108P5H8 polyclonal antibody as described in FIG. 20, using the respective cell lines expressing only the neomycin resistance gene as negative controls.

FIG. 25. 25A shows an alignment of 108P5H8 protein (SEQ ID.NO. : 2570) with the human zinc transporter 4, i.e. gi 11432533 (SEQ ID. NO. : 2579): 25B shows an alignment of 108P5H8 protein with the human zinc transporter ZNT4, i.e. gi 8134840 (SEQ ID. NO. : 2580): and 25C shows an alignment of 108P5H8 protein with the rat zinc transporter ZNT-4, i.e. gi 8134837 (SEQ ID. NO. : ?);.

FIG. 26. Detection of 108P5H8 protein by immunocytochemistry in LNCaP cells. Immunocytochemical staining of LNCaP cells (an androgen dependant prostate cancer cell line) showing expression of 108P5H8, which is not androgen regulated. LNCaP cell preparations were made from either cells grown in medium containing 10% fetal bovine serum (Panel A) or from cells grown for 72 hours in androgen free, serum depleted medium (by growing in charcoal dextran stripped medium) (Panel B) or from previously androgen starved cells which were subsequently stimulated with 10 mmol mibolerone, a synthetic androgen, for 48 hours (Panel C). LNCaP cells incubated with Rabbit IgG instead of rabbit antibody to 108P5H8 was included to show no non-specific binding of rabbit immunoglobulin to the cells (Panel D).

FIG. 27. Detection of 108P5H8 protein by immunohistochemistry in prostate cancer patient specimens. Immunohistochemical staining of frozen sections of a prostate carcinoma specimen (Gleason grade 6) showing expression of 108P5H8 in the neoplastic glands (Panel A) and no non-specific binding of rabbit immunoglobulin in the Rabbit IgG control (Panel B).

FIG. 28. FIGS. 28A & 28B show a vertical alignment comparison between nucleotide and amino acid sequences of the variants.

DETAILED DESCRIPTION OF THE INVENTION

Outline of Sections

I.) Definitions

II.) 108P5H8 Polynucleotides

-   -   II.A.) Uses of 108P5H8 Polynucleotides         -   II.A.1.) Monitoring of Genetic Abnormalities         -   II.A.2.) Antisense Embodiments         -   II.A.3.) Primers and Primer Pairs         -   II.A.4.) Isolation of 108P5H8-Encoding Nucleic Acid             Molecules         -   II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector             Systems

III.) 108P5H8-related Proteins

-   -   III.A.) Motif-bearing Protein Embodiments     -   III.B.) Expression of 108P5H8-related Proteins     -   III.C.) Modifications of 108P5H8-related Proteins     -   III.D.) Uses of 108P5H8-related Proteins

IV.) 108P5H8 Antibodies

V.) 108P5H8 Cellular Immune Responses

VI.) 108P5H8 Transgenic Animals

VII.) Methods for the Detection of 108P5H8

VIII.) Methods for Monitoring the Status of 108P5H8-related Genes and Their Products

IX.) Identification of Molecules That Interact With 108P5H8

X.) Therapeutic Methods and Compositions

-   -   X.A.) Anti-Cancer Vaccines     -   X.B.) 108P5H8 as a Target for Antibody-Based Therapy     -   X.C.) 108P5H8 as a Target for Cellular Immune Responses         -   X.C.1. Minigene Vaccines         -   X.C.2. Combinations of CTL Peptides with Helper Peptides         -   X.C.3. Combinations of CTL Peptides with T Cell Priming             Agents         -   X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL             and/or HTL Peptides     -   X.D.) Adoptive Immunotherapy     -   X.E.) Administration of Vaccines for Therapeutic or Prophylactic         Purposes

XI.) Diagnostic and Prognostic Embodiments of 108P5H8.

XII.) Inhibition of 108P5H8 Protein Function

-   -   XII.A.) Inhibition of 108P5H8 With Intracellular Antibodies     -   XII.B.) Inhibition of 108P5H8 with Recombinant Proteins     -   XII.C.) Inhibition of 108P5H8 Transcription or Translation     -   XII.D.) General Considerations for Therapeutic Strategies

XIII.) KITS

I.) Definitions:

Unless otherwise defined, all terms of art, notations and other scientific terms or terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this invention pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art. Many of the techniques and procedures described or referenced herein are well understood and commonly employed using conventional methodology by those skilled in the art, such as, for example, the widely utilized molecular cloning methodologies described in Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd. edition (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. As appropriate, procedures involving the use of commercially available kits and reagents are generally carried out in accordance with manufacturer defined protocols and/or parameters unless otherwise noted.

The terms “advanced prostate cancer”, “locally advanced prostate cancer”, “advanced disease” and “locally advanced disease” mean prostate cancers that have extended through the prostate capsule, and are meant to include stage C disease under the American Urological Association (AUA) system, stage C1-C2 disease under the Whitmore-Jewett system, and stage T3-T4 and N+ disease under the TNM (tumor, node, metastasis) system. In general, surgery is not recommended for patients with locally advanced disease, and these patients have substantially less favorable outcomes compared to patients having clinically localized (organ-confined) prostate cancer. Locally advanced disease is clinically identified by palpable evidence of induration beyond the lateral border of the prostate, or asymmetry or induration above the prostate base. Locally advanced prostate cancer is presently diagnosed pathologically following radical prostatectomy if the tumor invades or penetrates the prostatic capsule, extends into the surgical margin, or invades the seminal vesicles.

“Altering the native glycosylation pattern” is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence 108P5H8 (either by removing the underlying glycosylation site or by deleting the glycosylation by chemical and/or enzymatic means), and/or adding one or more glycosylation sites that are not present in the native sequence 108P5H8. In addition, the phrase includes qualitative changes in the glycosylation of the native proteins, involving a change in the nature and proportions of the various carbohydrate moieties present.

The term “analog” refers to a molecule which is structurally similar or shares similar or corresponding attributes with another molecule (e.g. a 108P5H8-related protein). For example an analog of a 108P5H8 protein can be specifically bound by an antibody or T cell that specifically binds to 108P5H8.

The term “antibody” is used in the broadest sense. Therefore an “antibody” can be naturally occurring or man-made such as monoclonal antibodies produced by conventional hybridoma technology. Anti-108P5H8 antibodies comprise monoclonal and polyclonal antibodies as well as fragments containing the antigen-binding domain and/or one or more complementarity determining regions of these antibodies.

An “antibody fragment” is defined as at least a portion of the variable region of the immunoglobulin molecule that binds to its target, i.e., the antigen-binding region. In one embodiment it specifically covers single anti-108P5H8 antibodies and clones thereof (including agonist, antagonist and neutralizing antibodies) and anti-108P5H8 antibody compositions with polyepitopic specificity.

The term “codon optimized sequences” refers to nucleotide sequences that have been optimized for a particular host species by replacing any codons having a usage frequency of less than about 20%. Nucleotide sequences that have been optimized for expression in a given host species by elimination of spurious polyadenylation sequences, elimination of exon/intron splicing signals, elimination of transposon-like repeats and/or optimization of GC content in addition to codon optimization are referred to herein as an “expression enhanced sequences.”

The term “cytotoxic agent” refers to a substance that inhibits or prevents the expression activity of cells, function of cells and/or causes destruction of cells. The term is intended to include radioactive isotopes chemotherapeutic agents, and toxins such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof. Examples of cytotoxic agents include, but are not limited to maytansinoids, yttrium, bismuth, ricin, ricin A-chain, doxorubicin, daunorubicin, taxol, ethidium bromide, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, dihydroxy anthracin dione, actinomycin, diphtheria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, modeccin A chain, alpha-sarcin, gelonin, mitogellin, retstrictocin, phenomycin, enomycin, curicin, crotin, calicheamicin, sapaonaria officinalis inhibitor, and glucocorticoid and other chemotherapeutic agents, as well as radioisotopes such as At²¹¹, I¹³¹, I¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi²¹², P³² and radioactive isotopes of Lu. Antibodies may also be conjugated to an anti-cancer pro-drug activating enzyme capable of converting the pro-drug to its active form.

The term “homolog” refers to a molecule which exhibits, homology to another molecule, by for example, having sequences of chemical residues that are the same or similar at corresponding positions.

“Human Leukocyte Antigen” or “HLA” is a human class I or class II Major Histocompatibility Complex (MHC) protein (see, e.g., Stites, et al., IMMUNOLOGY, 8^(TH) ED., Lange Publishing, Los Altos, Calif. (1994).

The terms “hybridize”, “hybridizing”, “hybridizes” and the like, used in the context of polynucleotides, are meant to refer to conventional hybridization conditions, preferably such as hybridization in 50% formamide/6×SSC/0.1% SDS/100 μg/ml ssDNA, in which temperatures for hybridization are above 37 degrees C. and temperatures for washing in 0.1×SSC/0.1% SDS are above 55 degrees C.

The phrases “isolated” or “biologically pure” refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment. For example, a polynucleotide is said to be “isolated” when it is substantially separated from contaminant polynucleotides that correspond or are complementary to genes other than the 108P5H8 genes or that encode polypeptides other than 108P5H8 gene product or fragments thereof. A skilled artisan can readily employ nucleic acid isolation procedures to obtain an isolated 108P5H8 polynucleotide. A protein is said to be “isolated,” for example, when physical, mechanical or chemical methods are employed to remove the 108P5H8 proteins from cellular constituents that are normally associated with the protein. A skilled artisan can readily employ standard purification methods to obtain an isolated 108P5H8 protein. Alternatively, an isolated protein can be prepared by chemical means.

The term “mammal” refers to any organism classified as a mammal, including mice, rats, rabbits, dogs, cats, cows, horses and humans. In one embodiment of the invention, the mammal is a mouse. In another embodiment of the invention, the mammal is a human.

The terms “metastatic prostate cancer” and “metastatic disease” mean prostate cancers that have spread to regional lymph nodes or to distant sites, and are meant to include stage D disease under the AUA system and stage T×N×M+ under the TNM system. As is the case with locally advanced prostate cancer, surgery is generally not indicated for patients with metastatic disease, and hormonal (androgen ablation) therapy is a preferred treatment modality. Patients with metastatic prostate cancer eventually develop an androgen-refractory state within 12 to 18 months of treatment initiation. Approximately half of these androgen-refractory patients die within 6 months after developing that status. The most common site for prostate cancer metastasis is bone. Prostate cancer bone metastases are often osteoblastic rather than osteolytic (i.e., resulting in net bone formation). Bone metastases are found most frequently in the spine, followed by the femur, pelvis, rib cage, skull and humerus. Other common sites for metastasis include lymph nodes, lung, liver and brain. Metastatic prostate cancer is typically diagnosed by open or laparoscopic pelvic lymphadenectomy, whole body radionuclide scans, skeletal radiography, and/or bone lesion biopsy.

The term “monoclonal antibody” refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the antibodies comprising the population are identical except for possible naturally occurring mutations that are present in minor amounts.

A “motif”, as in biological motif of an 108P5H8-related protein, refers to any pattern of amino acids forming part of the primary sequence of a protein, that is associated with a particular function (e.g. protein-protein interaction, protein-DNA interaction, etc) or modification (e.g. that is phosphorylated, glycosylated or amidated), or localization (e.g. secretory sequence, nuclear localization sequence, etc.) or a sequence that is correlated with being immunogenic, either humorally or cellularly. A motif can be either contiguous or capable of being aligned to certain positions that are generally correlated with a certain function or property. In the context of HLA motifs, “motif” refers to the pattern of residues in a peptide of defined length, usually a peptide of from about 8 to about 13 amino acids for a class I HLA motif and from about 6 to about 25 amino acids for a class II HLA motif, which is recognized by a particular HLA molecule. Peptide motifs for HLA binding are typically different for each protein encoded by each human HLA allele and differ in the pattern of the primary and secondary anchor residues.

A “pharmaceutical excipient” comprises a material such as an adjuvant, a carrier, pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservative, and the like.

“Pharmaceutically acceptable” refers to a non-toxic, inert, and/or composition that is physiologically compatible with humans or other mammals.

The term “polynucleotide” means a polymeric form of nucleotides of at least 10 bases or base pairs in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide, and is meant to include single and double stranded forms of DNA and/or RNA. In the art, this term if often used interchangeably with “oligonucleotide”. A polynucleotide can comprise a nucleotide sequence disclosed herein wherein thymidine (T), as shown for example in FIG. 2, can also be uracil (U); this definition pertains to the differences between the chemical structures of DNA and RNA, in particular the observation that one of the four major bases in RNA is uracil (U) instead of thymidine (T).

The term “polypeptide” means a polymer of at least about 4, 5, 6, 7, or 8 amino acids. Throughout the specification, standard three letter or single letter designations for amino acids are used. In the art, this term is often used interchangeably with “peptide” or “protein”.

An HLA “primary anchor residue” is an amino acid at a specific position along a peptide sequence which is understood to provide a contact point between the immunogenic peptide and the HLA molecule. One to three, usually two, primary anchor residues within a peptide of defined length generally defines a “motif” for an immunogenic peptide. These residues are understood to fit in close contact with peptide binding groove of an HLA molecule, with their side chains buried in specific pockets of the binding groove. In one embodiment, for example, the primary anchor residues for an HLA class I molecule are located at position 2 (from the amino terminal position) and at the carboxyl terminal position of a 8, 9, 10, 11, or 12 residue peptide epitope in accordance with the invention. In another embodiment, for example, the primary anchor residues of a peptide that will bind an HLA class II molecule are spaced relative to each other, rather than to the termini of a peptide, where the peptide is generally of at least 9 amino acids in length. The primary anchor positions for each motif and supermotif are set forth in Table IV. For example, analog peptides can be created by altering the presence or absence of particular residues in the primary and/or secondary anchor positions shown in Table IV. Such analogs are used to modulate the binding affinity and/or population coverage of a peptide comprising a particular HLA motif or supermotif.

A “recombinant” DNA or RNA molecule is a DNA or RNA molecule that has been subjected to molecular manipulation in vitro.

Non-limiting examples of small molecules include compounds that bind or interact with 108P5H8, ligands including hormones, neuropeptides, chemokines, odorants, phospholipids, and functional equivalents thereof that bind and preferably inhibit 108P5H8 protein function. Such non-limiting small molecules preferably have a molecular weight of less than about 10 kDa, more preferably below about 9, about 8, about 7, about 6, about 5 or about 4 kDa. In certain embodiments, small molecules physically associate with, or bind, 108P5H8 protein; are not found in naturally occurring metabolic pathways; and/or are more soluble in aqueous than non-aqueous solutions

“Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured nucleic acid sequences to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature that can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995).

“Stringent conditions” or “high stringency conditions”, as defined herein, are identified by, but not limited to, those that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; or (3) employ 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate),50 mM sodium phosphate (pH 6.8), 0.1% sodiumtpyrophosphate, 5× Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC (sodium chloride/sodium. citrate) and 50% formamide at 55° C., followed by a high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C. “Moderately stringent conditions” are described by, but not limited to, those in Sambrook et al., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and % SDS) less stringent than those described above. An example of moderately stringent conditions is overnight incubation at 37° C. in a solution comprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5× Denhardt's solution, 10% dextran sulfate, and 20 mg/mL denatured sheared salmon sperm DNA, followed by washing the filters in 1×SSC at about 37-50° C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.

An HLA “supermotif” is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles.

As used herein “to treat” or “therapeutic” and grammatically related terms, refer to any improvement of any consequence of disease, such as prolonged survival, less morbidity, and/or a lessening of side effects which are the byproducts of an alternative therapeutic modality; full eradication of disease is not required.

A “transgenic animal” (e.g., a mouse or rat) is an animal having cells that contain a transgene, which transgene was introduced into the animal or an ancestor of the animal at a prenatal, e.g., an embryonic stage. A “transgene” is a DNA that is integrated into the genome of a cell from which a transgenic animal develops.

As used herein, an HLA or cellular immune response “vaccine” is a composition that contains or encodes one or more peptides of the invention. There are numerous embodiments of such vaccines, such as a cocktail of one or more individual peptides; one or more peptides of the invention comprised by a polyepitopic peptide; or nucleic acids that encode such individual peptides or polypeptides, e.g., a minigene. that encodes a polyepitopic peptide. The “one or more peptides” can include any whole unit integer from 1-150 or more, e.g.; at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 150 or more peptides of the invention. The peptides or polypeptides can optionally be modified, such as by lipidation, addition of targeting or other sequences. HLA class I peptides of the invention can be admixed with, or linked to, HLA class II peptides, to facilitate activation of both cytotoxic T lymphocytes and helper T lymphocytes. HLA vaccines can also comprise peptide-pulsed antigen presenting cells, e.g., dendritic cells.

The term “variant” refers to a molecule that exhibits a variation from a described type or norm, such as a protein that has one or more different amino acid residues in the corresponding position(s) of a specifically described protein (e.g. the 108P5H8 protein shown in FIG. 2 or FIG. 3. An analog is an example of a variant protein. Splice isoforms and single nucleotides polymorphisms (SNPs) are further examples of variants.

The “108P5H8-related proteins” of the invention include those specifically identified herein, as well as allelic variants, conservative substitution variants, analogs and homologs that can be isolated/generated and characterized without undue experimentation following the methods outlined herein or readily available in the art. Fusion proteins that combine parts of different 108P5H8 proteins or fragments thereof, as well as fusion proteins of a 108P5H8 protein and a heterologous polypeptide are also included. Such 108P5H8 proteins are collectively referred to as the 108P5H8-related proteins, the proteins of the invention, or 108P5H8. The term “108P5H8-related protein” refers to a polypeptide fragment or an 108P5H8 protein sequence of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25 amino acids; or, at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100 or more than 100 amino acids.

II.) 108P5H8 Polynucleotides

One aspect of the invention provides polynucleotides corresponding or complementary to all or part of an 108P5H8 gene, mRNA, and/or coding sequence, preferably in isolated form, including polynucleotides encoding an 108P5H8-related protein and fragments thereof, DNA, RNA, DNA/RNA hybrid, and related molecules, polynucleotides or oligonucleotides complementary to an 108P5H8 gene or mRNA sequence or a part thereof, and polynucleotides or oligonucleotides that hybridize to an 108P5H8 gene, mRNA, or to an 108P5H8 encoding polynucleotide, (collectively, “108P5H8 polynucleotides”). In all instances when referred to in this section, T can also be U in FIG. 2.

Embodiments of a 108P5H8 polynucleotide include: a 108P5H8 polynucleotide having the sequence shown in FIG. 2, the nucleotide sequence of 108P5H8 as shown in FIG. 2 wherein T is U; at least 10 contiguous nucleotides of a polynucleotide having the sequence as shown in FIG. 2; or, at least 10 contiguous nucleotides of a polynucleotide having the sequence as shown in FIG. 2 where T is U. For example, embodiments of 108P5H8 nucleotides comprise, without limitation:

-   -   (I) a polynucleotide comprising, consisting essentially of, or         consisting of a sequence as shown in FIG. 2 (SEQ ID Nos.: 2569,         2571, & 2573), wherein T can also be U;     -   (II) a polynucleotide comprising, consisting essentially of, or         consisting of the sequence as shown in FIG. 2A (SEQ ID NO.:         2569), from nucleotide residue number 253 through nucleotide         residue number 1542, wherein T can also be U;     -   (III) a polynucleotide comprising, consisting essentially of, or         consisting of the sequence as shown in FIG. 2B (SEQ ID NO.:         2571), from nucleotide residue number 1 through nucleotide         residue number 1290, wherein T can also be U;     -   (IV) a polynucleotide comprising, consisting essentially of, or         consisting of the sequence as shown in FIG. 2C (SEQ ID NO.:         2573), from nucleotide residue number 1 through nucleotide         residue number 1290, wherein T can also be U;     -   (V) a polynucleotide that encodes an 108P5H8-related protein         that is at least 90% homologous to an entire amino acid sequence         shown in FIG. 2A-C (SEQ ID Nos.: 2570, 2572, & 2574);     -   (VI) a polynucleotide that encodes an 108P5H8-related protein         that is at least 90% identical to an entire amino acid sequence         shown in FIG. 2A-C (SEQ ID Nos.: 2570, 2572, & 2574);     -   (VII) a polynucleotide that encodes at least one peptide set         forth in Tables V-XVIII, XXII, and XXIII;     -   (VIII) a polynucleotide that encodes a peptide region of at         least 5 amino acids of a peptide of FIG. 3A or 3B in any whole         number increment up to 429 that includes an amino acid position         having a value greater than 0.5 in the Hydrophilicity profile of         FIG. 5;     -   (IX) a polynucleotide that encodes a peptide region of at least         5 amino acids of a peptide of FIG. 3A or 3B in any whole number         increment up to 429 that includes an amino acid position having         a value less than 0.5 in the Hydropathicity profile of FIG. 6;     -   (X) a polynucleotide that encodes a peptide region of at least 5         amino acids of a peptide of FIG. 3A or 3B in any whole number         increment up to 429 that includes an amino acid position having         a value greater than 0.5 in the Percent Accessible Residues         profile of FIG. 7;     -   (XI) a polynucleotide that encodes a peptide region of at least         5 amino acids of a peptide of FIG. 3A or 3B in any whole number         increment up to 429 that includes an amino acid position having         a value greater than 0.5 in the Average Flexibility profile on         FIG. 8;     -   (XII) a polynucleotide that encodes a peptide region of at least         5 amino acids of a peptide of FIG. 3A or 3B in any whole number         increment up to 429 that includes an amino acid position having         a value greater than 0.5 in the Beta-turn profile of FIG. 9;     -   (XIII) a polynucleotide that encodes a 108P5H8-related protein         whose sequence is encoded by the cDNAs contained in the plasmid         designated p108P5H8-C deposited with American Type Culture         Collection as Accession No. PTA-2198;     -   (XIV) a polynucleotide that is fully complementary to a         polynucleotide of any one of (I)-(XIII);     -   (XV) a polynucleotide that selectively hybridizes under         stringent conditions to a polynucleotide of (I)-(XIV);     -   (XVI) a peptide that is encoded by any of (I)-(XIII); and,     -   (XLII) a polynucleotide of any of (I)-(XV) or peptide of (XVI)         together with a pharmaceutical excipient and/or in a human unit         dose form.

As used herein, a range is understood to specifically disclose all whole unit positions thereof.

Typical embodiments of the invention disclosed herein include 108P5H8 polynucleotides that encode specific portions of 108P5H8 mRNA sequences (and those which are complementary to such sequences) such as those that encode the proteins and/or fragments thereof, for example:

4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 250, 275, 300, 325, 350, 375, 400, 425, or 429 contiguous amino acids of variants 1, 2 or 3.

For example, representative embodiments of the invention disclosed herein include: polynucleotides and their encoded-peptides themselves encoding about amino acid 1 to about amino acid 10of the 108P5H8 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 10 to about amino acid 20 of the 108P5H8 protein shown in FIG. 2, or FIG. 3, polynucleotides encoding about amino acid 20 to about amino acid 30 of the 108P5H8 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 30 to about amino acid 40 of the 108P5H8 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 40 to about amino acid 50 of the 108P5H8 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 50 to about amino acid 60 of the 108P5H8 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 60 to about amino acid 70 of the 108P5H8 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 70 to about amino acid 80 of the 108P5H8 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 80 to about amino acid 90 of the 108P5H8 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 90 to about amino acid 100 of the 108P5H8 protein shown in FIG. 2 or FIG. 3, in increments of about 10 amino acids, ending at the carboxyl terminal amino acid set forth in FIG. 2 or FIG. 3. Accordingly polynucleotides encoding portions of the amino acid sequence (of about 10 amino acids), of amino acids 100 through the carboxyl terminal amino acid of the 108P5H8 protein are embodiments of the invention. Wherein it is understood that each particular amino acid position discloses that position plus or minus five amino acid residues.

Polynucleotides encoding relatively long portions of a 108P5H8 protein are also within the scope of the invention. For example, polynucleotides encoding from about amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or 30, or 40 or 50 etc.) of the 108P5H8 protein shown in FIG. 2 or FIG. 3 can be generated by a variety of techniques well known in the art. These polynucleotide fragments can include any portion of the 108P5H8 sequence as shown in FIG. 2.

Additional illustrative embodiments of the invention disclosed herein include 108P5H8 polynucleotide fragments encoding one or more of the biological motifs contained within a 108P5H8 protein sequence, including one or more of the motif-bearing subsequences of a 108P5H8 protein set forth in Tables V-XVIII, XXII, and XXIII. In another embodiment, typical polynucleotide fragments of the invention encode one or more of the regions of 108P5H8 that exhibit homology to a known molecule. In another embodiment of the invention, typical polynucleotide fragments can encode one or more of the 108P5H8 N-glycosylation sites, cAMP and cGMP-dependent protein kinase phosphorylation sites, casein kinase II phosphorylation sites or N-myristoylation site and amidation sites.

II.A.) Uses of 108P5H8 Polynucleotides

II.A.1.) Monitoring of Genetic Abnormalities

The polynucleotides of the preceding paragraphs have a number of different specific uses. The human 108P5H8 gene maps to the chromosomal location set forth in Example 3. For example, because the 108P5H8 gene maps to this chromosome, polynucleotides that encode different regions of the 108P5H8 proteins are used to characterize cytogenetic abnormalities of this chromosomal locale, such as abnormalities that are identified as being associated with various cancers. In certain genes, a variety of chromosomal abnormalities including rearrangements have been identified as frequent cytogenetic abnormalities in a number of different cancers (see e.g. Krajinovic et al., Mutat. Res. 382(3-4): 81-83 (1998); Johansson et al., Blood 86(10): 3905-3914 (1995) and Finger et al., P.N.A.S. 85(23): 9158-9162 (1988)). Thus, polynucleotides encoding specific regions of the 108P5H8 proteins provide new tools that can be used to delineate, with greater precision than previously possible, cytogenetic abnormalities in the chromosomal region that encodes 108P5H8 that may contribute to the malignant phenotype. In this context, these polynucleotides satisfy a need in the art for expanding the sensitivity of chromosomal screening in order to identify more subtle and less common chromosomal abnormalities (see e.g. Evans et al., Am. J. Obstet. Gynecol 171(4): 1055-1057 (1994)).

Furthermore, as 108P5H8 was shown to be highly expressed in bladder and other cancers, 108P5H8 polynucleotides are used in methods assessing the status of 108P5H8 gene products in normal versus cancerous tissues. Typically, polynucleotides that encode specific regions of the 108P5H8 proteins are used to assess the presence of perturbations (such as deletions, insertions, point mutations, or alterations resulting in a loss of an antigen etc.) in specific regions of the 108P5H8 gene, such as regions containing one or more motifs. Exemplary assays include both RT-PCR assays as well as single-strand conformation polymorphism (SSCP) analysis (see, e.g., Marrogi et al., J. Cutan. Pathol. 26(8): 369-378 (1999), both of which utilize polynucleotides encoding specific regions of a protein to examine these regions within the protein.

II.A.2.) Antisense Embodiments

Other specifically contemplated nucleic acid related embodiments of the invention disclosed herein are genomic DNA, cDNAs, ribozymes, and antisense molecules, as well as nucleic acid molecules based on an alternative backbone, or including alternative bases, whether derived from natural sources or synthesized, and include molecules capable of inhibiting the RNA or protein expression of 108P5H8. For example, antisense molecules can be RNAs or other molecules, including peptide nucleic acids (PNAs) or non-nucleic acid molecules such as phosphorothioate derivatives, that specifically bind DNA or RNA in a base pair-dependent manner. A skilled artisan can readily obtain these classes of nucleic acid molecules using the 108P5H8 polynucleotides and polynucleotide sequences disclosed herein.

Antisense technology entails the administration of exogenous oligonucleotides that bind to a target polynucleotide located within the cells. The term “antisense” refers to the fact that such oligonucleotides are complementary to their intracellular targets, e.g., 108P5H8. See for example, Jack Cohen, Oligodeoxynucleotides, Antisense Inhibitors of Gene Expression, CRC Press, 1989; and Synthesis 1:1-5 (1988). The 108P5H8 antisense oligonucleotides of the present invention include derivatives such as S-oligonucleotides (phosphorothioate derivatives or S-oligos, see, Jack Cohen, supra), which exhibit enhanced cancer cell growth inhibitory action. S-oligos (nucleoside phosphorothioates) are isoelectronic analogs of an oligonucleotide (O-oligo) in which a nonbridging oxygen atom of the phosphate group is replaced by a sulfur atom. The S-oligos of the present invention can be prepared by treatment of the corresponding O-oligos with 3H-1,2-benzodithiol-3-one-1,1-dioxide, which is a sulfur transfer reagent. See, e.g., Iyer, R. P. et al., J. Org. Chem. 55:4693-4698 (1990); and Iyer, R. P. et al., J. Am. Chem. Soc. 112:1253-1254 (1990). Additional 108P5H8 antisense oligonucleotides of the present invention include morpholino antisense oligonucleotides known in the art (see, e.g., Partridge et al., 1996, Antisense & Nucleic Acid Drug Development 6: 169-175).

The 108P5H8 antisense oligonucleotides of the present invention typically can be RNA or DNA that is complementary to and stably hybridizes with the first 100 5′ codons or last 100 3′ codons of a 108P5H8 genomic sequence or the corresponding mRNA. Absolute complementarity is not required, although high degrees of complementarity are preferred. Use of an oligonucleotide complementary to this region allows for the selective hybridization to 108P5H8 mRNA and not to mRNA specifying other regulatory subunits of protein kinase. In one embodiment, 108P5H8 antisense oligonucleotides of the present invention are 15 to 30 -mer fragments of the antisense DNA molecule that have a sequence that hybridizes to 108P5H8 mRNA. Optionally, 108P5H8 antisense oligonucleotide is a 30 -mer oligonucleotide that is complementary to a region in the first 10 5′ codons or last 10 3′ codons of 108P5H8. Alternatively, the antisense molecules are modified to employ ribozymes in the inhibition of 108P5H8 expression, see, e.g., L. A. Couture & D. T. Stinchcomb; Trends Genet 12: 510-515 (1996).

II.A.3.) Primers and Primer Pairs

Further specific embodiments of this nucleotides of the invention include primers and primer pairs, which allow the specific amplification of polynucleotides of the invention or of any specific parts thereof, and probes that selectively or specifically hybridize to nucleic acid molecules of the invention or to any part thereof. Probes can be labeled with a detectable marker, such as, for example, a radioisotope, fluorescent compound, bioluminescent compound, a chemiluminescent compound, metal chelator or enzyme. Such probes and primers are used to detect the presence of a 108P5H8 polynucleotide in a sample and as a means for detecting a cell expressing a 108P5H8 protein.

Examples of such probes include polypeptides comprising all or part of the human 108P5H8 cDNA sequence shown in FIG. 2. Examples of primer pairs capable of specifically amplifying 108P5H8 mRNAs are also described in the Examples. As will be understood by the skilled artisan, a great many different primers and probes can be prepared based on the sequences provided herein and used effectively to amplify and/or detect a 108P5H8 mRNA.

The 108P5H8 polynucleotides of the invention are useful for a variety of purposes, including but not limited to their use as probes and primers for the amplification and/or detection of the 108P5H8 gene(s), mRNA(s), or fragments thereof; as reagents for the diagnosis and/or prognosis of prostate cancer and other cancers; as coding sequences capable of directing the expression of 108P5H8 polypeptides; as tools for modulating or inhibiting the expression of the 108P5H8 gene(s) and/or translation of the 108P5H8 transcript(s); and as therapeutic agents.

The present invention includes the use of any probe as described herein to identify and isolate a 108P5H8 or 108P5H8 related nucleic acid sequence from a naturally occurring source, such as humans or other mammals, as well as the isolated nucleic acid sequence per se, which would comprise all or most of the sequences found in the probe used.

II.A.4.) Isolation of 108P5H8-Encoding Nucleic Acid Molecules

The 108P5H8 cDNA sequences described herein enable the isolation of other polynucleotides encoding 108P5H8 gene product(s), as well as the isolation of polynucleotides encoding 108P5H8 gene product homologs, alternatively spliced isoforms, allelic variants, and mutant forms of a 108P5H8 gene product as well as polynucleotides that encode analogs of 108P5H8-related proteins. Various molecular cloning methods that can be employed to isolate full length cDNAs encoding an 108P5H8 gene are well known (see, for example, Sambrook, J. et al, Molecular Cloning: A Laboratory Manual, 2d edition, Cold Spring Harbor Press, New York, 1989; Current Protocols in Molecular Biology. Ausubel et al., Eds., Wiley and Sons, 1995). For example, lambda phage cloning methodologies can be conveniently employed, using commercially available cloning systems (e.g., Lambda ZAP Express, Stratagene). Phage clones containing 108P5H8 gene cDNAs can be identified by probing with a labeled 108P5H8 cDNA or a fragment thereof. For example, in one embodiment, a 108P5H8 cDNA (e.g., FIG. 2) or a portion thereof can be synthesized and used as a probe to retrieve overlapping and full-length cDNAs corresponding to a 108P5H8 gene. A 108P5H8 gene itself can be isolated by screening genomic DNA libraries, bacterial artificial chromosome libraries (BACs), yeast artificial chromosome libraries (YACs), and the like, with 108P5H8 DNA probes or primers.

II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector Systems

The invention also provides recombinant DNA or RNA molecules containing an 108P5H8 polynucleotide, a fragment, analog or homologue thereof, including but not limited to phages, plasmids, phagemids, cosmids, YACs, BACs, as well as various viral and non-viral vectors well known in the art, and cells transformed or transfected with such recombinant DNA or RNA molecules. Methods for generating such molecules are well known (see, for example, Sambrook et al., 1989, supra).

The invention further provides a host-vector system comprising a recombinant DNA molecule containing a 108P5H8 polynucleotide, fragment, analog or homologue thereof within a suitable prokaryotic or eukaryotic host cell. Examples of suitable eukaryotic host cells include a yeast cell, a plant cell, or an animal cell, such as a mammalian cell or an insect cell (e.g., a baculovirus-infectible cell such as an Sf9 or HighFive cell). Examples of suitable mammalian cells include various prostate cancer cell lines such as DU145 and TsuPr1, other transfectable or transducible prostate cancer cell lines, primary cells (PrEC), as well as a number of mammalian cells routinely used for the expression of recombinant proteins (e.g., COS, CHO, 293, 293T cells). More particularly, a polynucleotide comprising the coding sequence of 108P5H8 or a fragment, analog or homolog thereof can be used to generate 108P5H8 proteins or fragments thereof using any number of host-vector systems routinely used and widely known in the art.

A wide range of host-vector systems suitable for the expression of 108P5H8 proteins or fragments thereof are available, see for example, Sambrook et al., 1989, supra; Current Protocols in Molecular Biology, 1995, supra). Preferred vectors for mammalian expression include but are not limited to pcDNA 3.1 myc-His-tag (Invitrogen) and the retroviral vector pSRαtkneo (Muller et al., 1991, MCB 11:1785). Using these expression vectors, 108P5H8 can be expressed in several prostate cancer and non-prostate cell lines, including for example 293, 293T, rat-1, NIH 3T3 and TsuPr1. The host-vector systems of the invention are useful for the production of a 108P5H8 protein or fragment thereof. Such host-vector systems can be employed to study the functional properties of 108P5H8 and 108P5H8 mutations or analogs.

Recombinant human 108P5H8 protein or an analog or homolog or fragment thereof can be produced by mammalian cells transfected with a construct encoding a 108P5H8-related nucleotide. For example, 293T cells can be transfected with an expression plasmid encoding 108P5H8 or fragment, analog or homolog thereof, a 108P5H8-related protein is expressed in the 293T cells, and the recombinant 108P5H8 protein is isolated using standard purification methods (e.g., affinity purification using anti-108P5H8 antibodies). In another embodiment, a 108P5H8 coding sequence is subcloned into the retroviral vector pSRαMSVtkneo and used to infect various mammalian cell lines, such as NIH 3T3, TsuPr1, 293 and rat-1 in order to establish 108P5H8 expressing cell lines. Various other expression systems well known in the art can also be employed. Expression constructs encoding a leader peptide joined in frame to a 108P5H8 coding sequence can be used for the generation of a secreted form of recombinant 108P5H8 protein.

As discussed herein, redundancy in the genetic code permits variation in 108P5H8 gene sequences. In particular, it is known in the art that specific host species often have specific codon preferences, and thus one can adapt the disclosed sequence as preferred for a desired host. For example, preferred analog codon sequences typically have rare codons (i.e., codons having a usage frequency of less than about 20% in known sequences of the desired host) replaced with higher frequency codons. Codon preferences for a specific species are calculated, for example, by utilizing codon usage tables available on the INTERNET.

Additional sequence modifications are known to enhance protein expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon/intron splice site signals, transposon-like repeats, and/or other such well-characterized sequences that are deleterious to gene expression. The GC content of the sequence is adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. Where possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures. Other useful modifications include the addition of a translational initiation consensus sequence at the start of the open reading frame, as described in Kozak, Mol. Cell Biol., 9:5073-5080 (1989). Skilled artisans understand that the general rule that eukaryotic ribosomes initiate translation exclusively at the 5′ proximal AUG codon is abrogated only under rare conditions (see, e.g., Kozak PNAS 92(7): 2662-2666, (1995) and Kozak NAR 15(20): 8125-8148 (1987)).

III.) 108P5H8-Related Proteins

Another aspect of the present invention provides 108P5H8-related proteins. Specific embodiments of 108P5H8 proteins comprise a polypeptide having all or part of the amino acid sequence of human 108P5H8 as shown in FIG. 2 or FIG. 3. Alternatively, embodiments of 108P5H8 proteins comprise variant, homolog or analog polypeptides that have alterations in the amino acid sequence of 108P5H8 shown in FIG. 2 or FIG. 3.

In general, naturally occurring allelic variants of human 108P5H8 share a high degree of structural identity and homology (e.g., 90% or more homology). Typically, allelic variants of a 108P5H8 protein contain conservative amino acid substitutions within the 108P5H8 sequences described herein or contain a substitution of an amino acid from a corresponding position in a homologue of 108P5H8. One class of 108P5H8 allelic variants are proteins that share a high degree of homology with at least a small region of a particular 108P5H8 amino acid sequence, but further contain a radical departure from the sequence, such as a non-conservative substitution, truncation, insertion or frame shift. In comparisons of protein sequences, the terms, similarity, identity, and homology each have a distinct meaning as appreciated in the field of genetics. Moreover, orthology and paralogy can be important concepts describing the relationship of members of a given protein family in one organism to the members of the same family in other organisms.

Amino acid abbreviations are provided in Table II. Conservative amino acid substitutions can frequently be made in a protein without altering either the conformation or the function of the protein. Proteins of the invention can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 conservative substitutions. Such changes include substituting any of isoleucine (I), valine (V), and leucine (L) for any other of these hydrophobic amino acids; aspartic acid (D) for glutamic acid (E) and vice versa; glutamine (Q) for asparagine (N) and vice versa; and serine (S) for threonine (T) and vice versa. Other substitutions can also be considered conservative, depending on the environment of the particular amino acid and its role in the three-dimensional structure of the protein. For example, glycine (G) and alanine (A) can frequently be interchangeable, as can alanine (A) and valine (V). Methionine (M), which is relatively hydrophobic, can frequently be interchanged with leucine and isoleucine, and sometimes with valine. Lysine (K) and arginine (R) are frequently-interchangeable in locations in which the significant feature of the amino acid residue is its charge and the differing pK's of these two amino acid residues are not significant. Still other changes can be considered “conservative” in particular environments (see, e.g. Table III herein; pages 13-15 “Biochemistry” 2^(nd) ED. Lubert Stryer ed (Stanford University); Henikoff et al. PNAS 1992 Vol 89 10915-10919; Lei et al., J Biol Chem May 19, 1995; 270(20):11882-6).

Embodiments of the invention disclosed herein include a wide variety of art-accepted variants or analogs of 108P5H8 proteins such as polypeptides having amino acid insertions, deletions and substitutions. 108P5H8 variants can be made using methods known in the art such as site-directed mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis (Carter et al., Nucl. Acids Res., 13:4331 (1986); Zoller et al., Nucl. Acids Res., 10:6487 (1987)), cassette mutagenesis (Wells et al., Gene, 34:315 (1985)), restriction selection mutagenesis (Wells et al., Philos. Trans. R. Soc. London SerA, 317:415 (1986)) or other known techniques can be performed on the cloned DNA to produce the 108P5H8 variant DNA.

Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence that is involved in a specific biological activity such as a protein-protein interaction. Among the preferred scanning amino acids are relatively small, neutral amino acids. Such amino acids include alanine, glycine, serine, and cysteine. Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the variant. Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions (Creighton, The Proteins, (W.H. Freeman & Co., N.Y.); Chothia, J. Mol. Biol., 150:1 (1976)). If alanine substitution does not yield adequate amounts of variant, an isosteric amino acid can be used.

As defined herein, 108P5H8 variants, analogs or homologs, have the distinguishing attribute of having at least one epitope that is “cross reactive” with a 108P5H8 protein having an amino acid sequence of FIG. 3. As used in this sentence, “cross reactive” means that an antibody or T cell that specifically binds to an 108P5H8 variant also specifically binds to a 108P5H8 protein having an amino acid sequence set forth in FIG. 3. A polypeptide ceases to be a variant of a protein shown in FIG. 3, when it no longer contains any epitope capable of being recognized by an antibody or T cell that specifically binds to the starting 108P5H8 protein. Those skilled in the art understand that antibodies that recognize proteins bind to epitopes of varying size, and a grouping of the order of about four or five amino acids, contiguous or not, is regarded as a typical number of amino acids in a minimal epitope. See, e.g., Nair et al., J. Immunol 2000 165(12): 6949-6955; Hebbes et al., Mol Immunol (1989) 26(9):865-73; Schwartz et al, J Immunol (1985) 135(4):2598-608.

Other classes of 108P5H8-related protein variants share 70%, 75%, 80%, 85% or 90% or more similarity with an amino acid sequence of FIG. 3, or a fragment thereof. Another specific class of 108P5H8 protein variants or analogs comprise one or more of the 108P5H8 biological motifs described herein or presently known in the art. Thus, encompassed by the present invention are analogs of 108P5H8 fragments (nucleic or amino acid) that have altered functional (e.g. immunogenic) properties relative to the starting fragment. It is to be appreciated that motifs now or which become part of the art are to be applied to the nucleic or amino acid sequences of FIG. 2 or FIG. 3.

As discussed herein, embodiments of the claimed invention include polypeptides containing less than the full amino acid sequence of a 108P5H8 protein shown in FIG. 2 or FIG. 3. For example, representative embodiments of the invention comprise peptides/proteins having any 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more contiguous amino acids of a 108P5H8 protein shown in FIG. 2 or FIG. 3.

Moreover, representative embodiments of the invention disclosed herein include polypeptides consisting of about amino acid 1 to about amino acid 10 of a 108P5H8 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 10 to about amino acid 20 of a 108P5H8 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 20 to about amino acid 30 of a 108P5H8 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 30 to about amino acid 40 of a 108P5H8 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 40 to about amino acid 50 of a 108P5H8 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 50 to about amino acid 60 of a 108P5H8 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 60 to about amino acid 70 of a 108P5H8 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 70 to about amino acid 80 of a 108P5H8 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 80 to about amino acid 90 of a 108P5H8 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 90 to about amino acid 100 of a 108P5H8 protein shown in FIG. 2 or FIG. 3, etc. throughout the entirety of a 108P5H8 amino acid sequence. Moreover, polypeptides consisting of about amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or 130, or 140 or 150 etc.) of a 108P5H8 protein shown in FIG. 2 or FIG. 3 are embodiments of the invention. It is to be appreciated that the starting and stopping positions in this paragraph refer to the specified position as well as that position plus or minus 5 residues.

108P5H8-related proteins are generated using standard peptide synthesis technology or using chemical cleavage methods well known in the art. Alternatively, recombinant methods can be used to generate nucleic acid molecules that encode a 108P5H8-related protein. In one embodiment, nucleic acid molecules provide a means to generate defined fragments of a 108P5H8 protein (or variants, homologs or analogs thereof).

III.A.) Motif-Bearing Protein Embodiments

Additional illustrative embodiments of the invention disclosed herein include 108P5H8 polypeptides comprising the amino acid residues of one or more of the biological motifs contained within a 108P5H8 polypeptide sequence set forth in FIG. 2 or FIG. 3. Various motifs are known in the art, and a protein can be evaluated for the presence of such motifs by a number of publicly available Internet sites (see, e.g., Epimatrix₁₉₈ and Epimer_(™), Brown University, and BIMAS).

Motif bearing subsequences of all 108P5H8 variant proteins are set forth and identified in Table XIX.

Table XX sets forth several frequently occurring motifs based on pfam searches. The columns of Table XX list (1) motif name abbreviation, (2) percent identity found amongst the different member of the motif family, (3) motif name or description and (4) most common function; location information is included if the motif is relevant for location.

Polypeptides comprising one or more of the 108P5H8 motifs discussed above are useful in elucidating the specific characteristics of a malignant phenotype in view of the observation that the 108P5H8 motifs discussed above are associated with growth dysregulation and because 108P5H8 is overexpressed in certain cancers (See, e.g., Table I). Casein kinase II, cAMP and camp-dependent protein kinase, and Protein Kinase C, for example, are enzymes known to be associated with the development of the malignant phenotype (see e.g. Chen et al., Lab Invest., 78(2): 165-174 (1998); Gaiddon et al., Endocrinology 136(10): 4331-4338 (1995); Hall et al., Nucleic Acids Research 24(6): 1119-1126 (1996); Peterziel et al., Oncogene 18(46): 6322-6329 (1999) and O'Brian, Oncol. Rep. 5(2): 305-309 (1998)). Moreover, both glycosylation and myristoylation are protein modifications also associated with cancer and cancer progression (see e.g. Dennis et al., Biochem. Biophys. Acta 1473(1):21-34 (1999); Raju et al., Exp. Cell Res. 235(1): 145-154 (1997)). Amidation is another protein modification also associated with cancer and cancer progression (see e.g. Treston et al., J. Natl. Cancer Inst. Monogr. (13): 169-175 (1992)).

In another embodiment, proteins of the invention comprise one or more of the immunoreactive epitopes identified in accordance with art-accepted methods, such as the peptides set forth in Tables V-XVIII, XXII, and XXIII. CTL epitopes can be determined using specific algorithms to identify peptides within an 108P5H8 protein that are capable of optimally binding to specified HLA alleles (e.g., Table IV; Epimatrix™ and Epimer™, Brown University, and BIMAS.) Moreover, processes for identifying peptides that have sufficient binding affinity for HLA molecules and which are correlated with being immunogenic epitopes, are well known in the art, and are carried out without undue experimentation. In addition, processes for identifying peptides that are immunogenic epitopes, are well known in the art, and are carried out without undue experimentation either in vitro or in vivo.

Also known in the art are principles for creating analogs of such epitopes in order to modulate immunogenicity. For example, one begins with an epitope that bears a CTL or HTL motif (see, e.g., the HLA Class I and HLA Class II motifs/supermotifs of Table IV). The epitope is analoged by substituting out an amino acid at one of the specified positions, and replacing it with another amino acid specified for that position. For example, one can substitute out a deleterious residue in favor of any other residue, such as a preferred residue as defined in Table IV; substitute a less-preferred residue with a preferred residue as defined in Table IV; or substitute an originally-occurring preferred residue with another preferred residue as defined in Table IV. Substitutions can occur at primary anchor positions or at other positions in a peptide; see, e.g., Table IV.

A variety of references reflect the art regarding the identification and generation of epitopes in a protein of interest as well as analogs thereof. See, for example, WO 9733602 to Chesnut et al.; Sette, Immunogenetics 1999 50(3-4): 201-212; Sette et al., J. Immunol. 2001 166(2): 1389-1397; Sidney et al., Hum. Immunol. 1997 58(1): 12-20; Kondo et al., Immunogenetics 1997 45(4): 249-258; Sidney et al., J. Immunol. 1996 157(8): 3480-90; and Falk et al., Nature 351: 290-6 (1991); Hunt et al., Science 255:1261-3 (1992); Parker et al., J. Immunol. 149:3580-7 (1992); Parker et al., J. Immunol. 152:163-75 (1994); Kast et al., 1994 152(8): 3904-12; Borras-Cuesta et al., Hum. Immunol. 2000 61(3): 266-278; Alexander et al., J. Immunol. 2000 164(3); 164(3): 1625-1633; Alexander et al., PMID: 7895164, UI: 95202582; O'Sullivan et al., J. Immunol. 1991 147(8): 2663-2669; Alexander et al., Immunity 1994 1(9): 751-761 and Alexander et al., Immunol. Res. 1998 18(2): 79-92.

Related embodiments of the inventions include polypeptides comprising combinations of the different motifs set forth in Table XIX, and/or, one or more of the predicted CTL epitopes of Tables V-XVIII, Table XXII, Table XXIII, and/or, one or more of the T cell binding motifs known in the art. Preferred embodiments contain no insertions, deletions or substitutions either within the motifs or the intervening sequences of the polypeptides. In addition, embodiments which include a number of either N-terminal and/or C-terminal amino acid residues on either side of these motifs may be desirable (to, for example, include a greater portion of the polypeptide architecture in which the motif is located). Typically the number of N-terminal and/or C-terminal amino acid residues on either side of a motif is between about 1 to about 100 amino acid residues, preferably 5 to about 50 amino acid residues.

108P5H8-related proteins are embodied in many forms, preferably in isolated form. A purified 108P5H8 protein molecule will be substantially free of other proteins or molecules that impair the binding of 108P5H8 to antibody, T cell or other ligand. The nature and degree of isolation and purification will depend on the intended use. Embodiments of a 108P5H8-related proteins include purified 108P5H8-related proteins and functional, soluble 108P5H8-related proteins. In one embodiment, a functional, soluble 108P5H8 protein or fragment thereof retains the ability to be bound by antibody, T cell or other ligand.

The invention also provides 108P5H8 proteins comprising biologically active fragments of a 108P5H8 amino acid sequence shown in FIG. 2 or FIG. 3. Such proteins exhibit properties of the starting 108P5H8 protein, such as the ability to elicit the generation of antibodies that specifically bind an epitope associated with the starting 108P5H8 protein; to be bound by such antibodies; to elicit the activation of HTL or CTL; and/or, to be recognized by HTL or CTL that also specifically bind to the starting protein.

108P5H8-related polypeptides that contain particularly interesting structures can be predicted and/or identified using various analytical techniques well known in the art, including, for example, the methods of Chou-Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis, or on the basis of immunogenicity. Fragments that contain such structures are particularly useful in generating subunit-specific anti-108P5H8 antibodies, or T cells or in identifying cellular factors that bind to 108P5H8.

CTL epitopes can be determined using specific algorithms to identify peptides within an 108P5H8 protein that are capable of optimally binding to specified HLA alleles (e.g., by using the SYFPEITHI site at World Wide Web; the listings in Table IV(A)-(E); Epimatrix™ and Epimer™, Brown University and BIMAS). Illustrating this, peptide epitopes from 108P5H8 that are presented in the context of human MHC class I molecules HLA-A1, A2, A3, A11, A24, B7 and B35 were predicted (Tables V-XVIII, XXII, and XXIII). Specifically, the complete amino acid sequence of the 108P5H8 protein and relevant portions of other variants, i.e., for HLA Class I predictions 9 flanking residues on either side of a point mutation, and for HLA Class II predictions 14 flanking residues on either side of a point mutation, were entered into the HLA Peptide Motif Search algorithm found in the Bioinformatics and Molecular Analysis Section (BIMAS) web site listed above; for HLA Class II the site SYFPEITHI was used.

The HLA peptide motif search algorithm was developed by Dr. Ken Parker based on binding of specific peptide sequences in the groove of HLA Class I molecules, in particular HLA-A2 (see, e.g., Falk et al., Nature 351: 290-6 (1991); Hunt et al., Science 255:1261-3 (1992); Parker et al., J. Immunol. 149:3580-7(1992); Parker et al., J. Immunol. 152:163-75 (1994)). This algorithm allows location and ranking of 8 -mer, 9 -mer, and 10 -mer peptides from a complete protein sequence for predicted binding to HLA-A2 as well as numerous other HLA Class I molecules. Many HLA class I binding peptides are 8-, 9-, 10 or 11 -mers. For example, for class I HLA-A2, the epitopes preferably contain a leucine (L) or methionine (M) at position 2 and a valine (V) or leucine (L) at the C-terminus (see, e.g., Parker et al., J. Immunol. 149:3580-7 (1992)). Selected results of 108P5H8 predicted binding peptides are shown in Tables V-XVIII, XXII, and XXIII herein. In Tables V-XVIII, the top 50 ranking candidates, 9 -mers and 10 -mers, for each family member are shown along with their location, the amino acid sequence of each specific peptide, and an estimated binding score. The binding score corresponds to the estimated half time of dissociation of complexes containing the peptide at 37° C. at pH 6.5. Peptides with the highest binding score are predicted to be the most tightly bound to HLA Class I on the cell surface for the greatest period of time and thus represent the best immunogenic targets for T-cell recognition.

Actual binding of peptides to an HLA allele can be evaluated by stabilization of HLA expression on the antigen-processing defective cell line T2 (see, e.g., Xue et al., Prostate 30:73-8 (1997) and Peshwa et al., Prostate 36:129-38 (1998)). Immunogenicity of specific peptides can be evaluated in vitro by stimulation of CD8+ cytotoxic T lymphocytes (CTL) in the presence of antigen presenting cells such as dendritic cells.

It is to be appreciated that every epitope predicted by the BIMAS site, Epimer™ and Epimatrix™ sites, or specified by the HLA class I or class II motifs available in the art or which become part of the art such as set forth in Table IV (or determined using World Wide Web site URL syfpeithi.bmi-heidelberg.com/, or BIMAS, bimas.dcrt.nih.gov/) are to be “applied” to a 108P5H8 protein in accordance with the invention. As used in this context “applied” means that a 108P5H8 protein is evaluated, e.g., visually or by computer-based patterns finding methods, as appreciated by those of skill in the relevant art. Every subsequence of a 108P5H8 protein of 8, 9, 10, or 11 amino acid residues that bears an HLA Class I motif, or a subsequence of 9 or more amino acid residues that bear an HLA Class II motif are within the scope of the invention.

III.B.) Expression of 108P5H8-Related Proteins

In an embodiment described in the examples that follow, 108P5H8 can be conveniently expressed in cells (such as 293T cells) transfected with a commercially available expression vector such as a CMV-driven expression vector encoding 108P5H8 with a C-terminal 6×His and MYC tag (pcDNA3.1/mycHIS, Invitrogen or Tag5, GenHunter Corporation, Nashville Tenn.). The Tag5 vector provides an IgGK secretion signal that can be used to facilitate the production of a secreted 108P5H8 protein in transfected cells. The secreted HIS-tagged 108P5H8 in the culture media can be purified, e.g., using a nickel column using standard techniques.

III.C.) Modifications of 108P5H8-Related Proteins

Modifications of 108P5H8-related proteins such as covalent modifications are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a 108P5H8 polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues of a 108P5H8 protein. Another type of covalent modification of a 108P5H8 polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of a protein of the invention. Another type of covalent modification of 108P5H8 comprises linking a 108P5H8 polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Pat. Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337.

The 108P5H8-related proteins of the present invention can also be modified to form a chimeric molecule comprising 108P5H8 fused to another, heterologous polypeptide or amino acid sequence. Such a chimeric molecule can be synthesized chemically or recombinantly. A chimeric molecule can have a protein of the invention fused to another tumor-associated antigen or fragment thereof. Alternatively, a protein in accordance with the invention can comprise a fusion of fragments of a 108P5H8 sequence (amino or nucleic acid) such that a molecule is created that is not, through its length, directly homologous to the amino or nucleic acid sequences shown in FIG. 2 or FIG. 3. Such a chimeric molecule can comprise multiples of the same subsequence of 108P5H8. A chimeric molecule can comprise a fusion of a 108P5H8-related protein with a polyhistidine epitope tag, which provides an epitope to which immobilized nickel can selectively bind, with cytokines or with growth factors. The epitope tag is generally placed at the amino- or carboxyl-terminus of a 108P5H8 protein. In an alternative embodiment, the chimeric molecule can comprise a fusion of a 108P5H8-related protein with an immunoglobulin or a particular region of an immunoglobulin. For a bivalent form of the chimeric molecule (also referred to as an “immunoadhesin”), such a fusion could be to the Fe region of an IgG molecule. The Ig fusions preferably include the substitution of a soluble (transmembrane domain deleted or inactivated) form of a 108P5H8 polypeptide in place of at least one variable region within an Ig molecule. In a preferred embodiment, the immunoglobulin fusion includes the hinge, CH2 and CH3, or the hinge, CHI, CH2 and CH3 regions of an IgGI molecule. For the production of immunoglobulin fusions see, e.g., U.S. Pat. No. 5,428,130 issued Jun. 27, 1995.

III.D.) Uses of 108P5H8-Related Proteins

The proteins of the invention have a number of different specific uses. As 108P5H8 is highly expressed in prostate and other cancers, 108P5H8-related proteins are used in methods that assess the status of 108P5H8 gene products in normal versus cancerous tissues, thereby elucidating the malignant phenotype. Typically, polypeptides from specific regions of a 108P5H8 protein are used to assess the presence of perturbations (such as deletions, insertions, point mutations etc.) in those regions (such as regions containing one or more motifs). Exemplary assays utilize antibodies or T cells targeting 108P5H8-related proteins comprising the amino acid residues of one or more of the biological motifs contained within a 108P5H8 polypeptide sequence in order to evaluate the characteristics of this region in normal versus cancerous tissues or to elicit an immune response to the epitope. Alternatively, 108P5H8-related proteins that contain the amino acid residues of one or more of the biological motifs in a 108P5H8 protein are used to screen for factors that interact with that region of 108P5H8.

108P5H8 protein fragments/subsequences are particularly useful in generating and characterizing domain-specific antibodies (e.g., antibodies recognizing an extracellular or intracellular epitope of an 108P5H8 protein), for identifying agents or cellular factors that bind to 108P5H8 or a particular structural domain thereof, and in various therapeutic and diagnostic contexts, including but not limited to diagnostic assays, cancer vaccines and methods of preparing such vaccines.

Proteins encoded by the 108P5H8 genes, or by analogs, homologs or fragments thereof, have a variety of uses, including but not limited to generating antibodies and in methods for identifying ligands and other agents and cellular constituents that bind to an 108P5H8 gene product. Antibodies raised against an 108P5H8 protein or fragment thereof are useful in diagnostic and prognostic assays, and imaging methodologies in the management of human cancers characterized by expression of 108P5H8 protein, such as those listed in Table I. Such antibodies can be expressed intracellularly and used in methods of treating patients with such cancers. 108P5H8-related nucleic acids or proteins are also used in generating HTL or CTL responses.

Various immunological assays useful for the detection of 108P5H8 proteins are used, including but not limited to various types of radioimmunoassay, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA), immunocytochemical methods, and the like. Antibodies can be labeled and used as immunological imaging reagents capable of detecting 108P5H8-expressing cells (e.g., in radioscintigraphic imaging methods). 108P5H8 proteins are also particularly useful in generating cancer vaccines, as further described herein.

IV.) 108P5H8 Antibodies

Another aspect of the invention provides antibodies that bind to 108P5H8-related proteins. Preferred antibodies specifically bind to a 108P5H8-related protein and do not bind (or bind weakly) to peptides or proteins that are not 108P5H8-related proteins. For example, antibodies that bind 108P5H8 can bind 108P5H8-related proteins such as the homologs or analogs thereof.

108P5H8 antibodies of the invention are particularly useful in cancer (see, e.g., Table I) diagnostic and prognostic assays, and imaging methodologies. Similarly, such antibodies are useful in the treatment, diagnosis, and/or prognosis of other cancers, to the extent 108P5H8 is also expressed or overexpressed in these other cancers. Moreover, intracellularly expressed antibodies (e.g., single chain antibodies) are therapeutically useful in treating cancers in which the expression of 108P5H8 is involved, such as advanced or metastatic prostate cancers.

The invention also provides various immunological assays useful for the detection and quantification of 108P5H8 and mutant 108P5H8-related proteins. Such assays can comprise one or more 108P5H8 antibodies capable of recognizing and binding a 108P5H8-related protein, as appropriate. These assays are performed within various immunological assay formats well known in the art, including but not limited to various types of radioimmunoassays, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA), and the like.

Immunological non-antibody assays of the invention also comprise T cell immunogenicity assays (inhibitory or stimulatory) as well as major histocompatibility complex (MHC) binding assays.

In addition, immunological imaging methods capable of detecting prostate cancer and other cancers expressing 108P5H8 are also provided by the invention, including but not limited to radioscintigraphic imaging methods using labeled 108P5H8 antibodies. Such assays are clinically useful in the detection, monitoring, and prognosis of 108P5H8 expressing cancers such as prostate cancer.

108P5H8 antibodies are also used in methods for purifying a 108P5H8-related protein and for isolating 108P5H8 homologues and related molecules. For example, a method of purifying a 108P5H8-related protein comprises incubating an 108P5H8 antibody, which has been coupled to a solid matrix, with a lysate or other solution containing a 108P5H8-related protein under conditions that permit the 108P5H8 antibody to bind to the 108P5H8-related protein; washing the solid matrix to eliminate impurities; and eluting the 108P5H8-related protein from the coupled antibody. Other uses of 108P5H8 antibodies in accordance with the invention include generating anti-idiotypic antibodies that mimic a 108P5H8 protein.

Various methods for the preparation of antibodies are well known in the art. For example, antibodies can be prepared by immunizing a suitable mammalian host using a 108P5H8-related protein, peptide, or fragment, in isolated or immunoconjugated form (Antibodies: A Laboratory Manual, CSH Press, Eds., Harlow, and Lane (1988); Harlow, Antibodies, Cold Spring Harbor Press, NY (1989)). In addition, fusion proteins of 108P5H8 can also be used, such as a 108P5H8 GST-fusion protein. In a particular embodiment, a GST fusion protein comprising all or most of the amino acid sequence of FIG. 2 or FIG. 3 is produced, then used as an immunogen to generate appropriate antibodies. In another embodiment, a 108P5H8-related protein is synthesized and used as an immunogen.

In addition, naked DNA immunization techniques known in the art are used (with or without purified 108P5H8-related protein or 108P5H8 expressing cells) to generate an immune response to the encoded immunogen (for review, see Donnelly et al., 1997, Ann. Rev. Immunol. 15: 617-648).

The amino acid sequence of a 108P5H8 protein as shown in FIG. 2 or FIG. 3 can be analyzed to select specific regions of the 108P5H8 protein for generating antibodies. For example, hydrophobicity and hydrophilicity analyses of a 108P5H8 amino acid sequence are used to identify hydrophilic regions in the 108P5H8 structure. Regions of a 108P5H8 protein that show immunogenic structure, as well as other regions and domains, can readily be identified using various other methods known in the art, such as Chou-Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis. Thus, each region identified by any of these programs or methods is within the scope of the present invention. Methods for the generation of 108P5H8 antibodies are further illustrated by way of the examples provided herein. Methods for preparing a protein or polypeptide for use as an immunogen are well known in the art. Also well known in the art are methods for preparing immunogenic conjugates of a protein with a carrier, such as BSA, KLH or other carrier protein. In some circumstances, direct conjugation using, for example, carbodiimide reagents are used; in other instances lining reagents such as those supplied by Pierce Chemical Co., Rockford, Ill., are effective. Administration of a 108P5H8 immunogen is often conducted by injection over a suitable time period and with use of a suitable adjuvant, as is understood in the art. During the immunization schedule, titers of antibodies can be taken to determine adequacy of antibody formation.

108P5H8 monoclonal antibodies can be produced by various means well known in the art. For example, immortalized cell lines that secrete a desired monoclonal antibody are prepared using the standard hybridoma technology of Kohler and Milstein or modifications that immortalize antibody-producing B cells, as is generally known. Immortalized cell lines that secrete the desired antibodies are screened by immunoassay in which the antigen is a 108P5H8-related protein. When the appropriate immortalized cell culture is identified, the cells can be expanded and antibodies produced either from in vitro cultures or from ascites fluid.

The antibodies or fragments of the invention can also be produced, by recombinant means. Regions that bind specifically to the desired regions of a 108P5H8 protein can also be produced in the context of chimeric or complementarity determining region (CDR) grafted antibodies of multiple species origin. Humanized or human 108P5H8 antibodies can also be produced, and are preferred for use in therapeutic contexts. Methods for humanizing murine and other non-human antibodies, by substituting one or more of the non-human antibody CDRs for corresponding human antibody sequences, are well known (see for example, Jones et al., 1986, Nature 321: 522-525; Riechmann et al., 1988, Nature 332: 323-327; Verhoeyen et al., 1988, Science 239: 1534-1536). See also, Carter et al., 1993, Proc. Natl. Acad. Sci. USA 89: 4285 and Sims et al., 1993, J. Immunol. 151: 2296.

Methods for producing fully human monoclonal antibodies include phage display and transgenic methods (for review, see Vaughan et al., 1998, Nature Biotechnology 16: 535-539). Fully human 108P5H8 monoclonal antibodies can be generated using cloning technologies employing large human Ig gene combinatorial libraries (i.e., phage display) (Griffiths and Hoogenboom, Building an in vitro immune system: human antibodies from phage display libraries. In: Protein Engineering of Antibody Molecules for Prophylactic and Therapeutic Applications in Man, Clark, M. (Ed.), Nottingham Academic, pp 45-64 (1993); Burton and Barbas, Human Antibodies from combinatorial libraries. Id., pp 65-82). Fully human 108P5H8 monoclonal antibodies can also be produced using transgenic mice engineered to contain human immunoglobulin gene loci as described in PCT Patent Application WO98/24893, Kucherlapati and Jakobovits et al., published Dec. 3, 1997 (see also, Jakobovits, 1998, Exp. Opin. Invest. Drugs 7(4): 607-614; U.S. Pat. No. 6,162,963 issued 19 Dec. 2000; U.S. Pat. No. 6,150,584 issued 12 Nov. 2000; and, U.S. Pat. No. 6,114,598 issued 5 Sep. 2000). This method avoids the in vitro manipulation required with phage display technology and efficiently produces high affinity authentic human antibodies.

Reactivity of 108P5H8 antibodies with an 108P5H8-related protein can be established by a number of well known means, including Western blot, immunoprecipitation, ELISA, and FACS analyses using, as appropriate, 108P5H8-related proteins, 108P5H8-expressing cells or extracts thereof. A 108P5H8 antibody or fragment thereof can be labeled with a detectable marker or conjugated to a second molecule. Suitable detectable markers include, but are not limited to, a radioisotope, a fluorescent compound, a bioluminescent compound, chemiluminescent compound, a metal chelator or an enzyme. Further, bi-specific antibodies specific for two or more 108P5H8 epitopes are generated using methods generally known in the art. Homodimeric antibodies can also be generated by cross-linking techniques known in the art (e.g., Wolff et al., Cancer Res. 53: 2560-2565).

V.) 108P5H8 Cellular Immune Responses

The mechanism by which T cells recognize antigens has been delineated. Efficacious peptide epitope vaccine compositions of the invention induce a therapeutic or prophylactic immune responses in very broad segments of the world-wide population. For an understanding of the value and efficacy of compositions of the invention that induce cellular immune responses, a brief review of immunology-related technology is provided.

A complex of an HLA molecule and a peptidic antigen acts as the ligand recognized by HLA-restricted T cells (Buus, S. et al., Cell 47:1071, 1986; Babbitt, B. P. et al., Nature 317:359, 1985; Townsend, A. and Bodmer, H., Annu. Rev. Immunol. 7:601, 1989; Germain, R. N., Annu. Rev. Immunol. 11:403, 1993). Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues that correspond to motifs required for specific binding to HLA antigen molecules have been identified and are set forth in Table IV (see also, e.g., Southwood, et al., J. Immunol. 160:3363, 1998; Rammensee, et al., Immunogenetics 41:178, 1995; Rammensee et al., SYFPEITHI, access via World Wide Web at URL syfpeithi.bmi-heidelberg.com/; Sette, A. and Sidney, J. Curr. Opin. Immunol. 10:478, 1998; Engelhard, V. H., Curr. Opin. Immunol. 6:13, 1994; Sette, A. and Grey, H. M., Curr. Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J. Curr. Biol. 6:52, 1994; Ruppert et al., Cell 74:929-937, 1993; Kondo et al., J. Immunol. 155:4307-4312, 1995; Sidney et al., J. Immunol. 157:3480-3490, 1996; Sidney et al., Human Immunol. 45:79-93, 1996; Sette, A. and Sidney, J. Immunogenetics 1999 November; 50(3-4):201-12, Review).

Furthermore, x-ray crystallographic analyses of HLA-peptide complexes have revealed pockets within the peptide binding cleft/groove of HLA molecules which accommodate, in an allele-specific mode, residues borne by peptide ligands; these residues in turn determine the HLA binding capacity of the peptides in which they are present. (See, e.g., Madden, D. R. Annu. Rev. Immunol. 13:587, 1995; Smith, et al., Immunity 4:203, 1996; Fremont et al., Immunity 8:305, 1998; Stern et al., Structure 2:245, 1994; Jones, E. Y. Curr. Opin. Immunol. 9:75, 1997; Brown, J. H. et al., Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl. Acad. Sci. USA 90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992; Silver, M. L. et al., Nature 360:367, 1992; Matsumura, M. et al., Science 257:927, 1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H. et al., Science 257:919, 1992; Saper, M. A., Bjorkman, P. J. and Wiley, D. C., J. Mol. Biol. 219:277, 1991.)

Accordingly, the definition of class I and class II allele-specific HLA binding motifs, or class I or class II supermotifs allows identification of regions within a protein that are correlated with binding to particular HLA antigen(s).

Thus, by a process of HLA motif identification, candidates for epitope-based vaccines have been identified; such candidates can be further evaluated by HLA-peptide binding assays to determine binding affinity and/or the time period of association of the epitope and its corresponding HLA molecule. Additional confirmatory work can be performed to select, amongst these vaccine candidates, epitopes with preferred characteristics in terms of population coverage, and/or immunogenicity.

Various strategies can be utilized to evaluate cellular immunogenicity, including:

1) Evaluation of primary T cell cultures from normal individuals (see, e.g., Wentworth, P. A. et al., Mol. Immunol. 32:603, 1995; Celis, E. et al., Proc. Natl. Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J. Immunol. 158-1796, 1997; Kawashima, I. et al., Human Immunol. 59:1, 1998). This procedure involves the stimulation of peripheral blood lymphocytes (PBL) from normal subjects with a test peptide in the presence of antigen presenting cells in vitro over a period of several weeks. T cells specific for the peptide become activated during this time and are detected using, e.g., a lymphokine- or ⁵¹Cr-release assay involving peptide sensitized target cells.

2) Immunization of HLA transgenic mice (see, e.g., Wentworth, P. A. et al., J. Immunol. 26:97, 1996; Wentworth, P. A. et al., Int. Immunol. 8:651, 1996; Alexander, J. et al., J. Immunol. 159:4753, 1997). For example, in such methods peptides in incomplete Freund's adjuvant are administered subcutaneously to HLA transgenic mice. Several weeks following immunization, splenocytes are removed and cultured in vitro in the presence of test peptide for approximately one week. Peptide-specific T cells are detected using, e.g., a ⁵¹Cr-release assay involving peptide sensitized target cells and target cells expressing endogenously generated antigen.

3) Demonstration of recall T cell responses from immune individuals who have been either effectively vaccinated and/or from chronically ill patients (see, e.g., Rehermann, B. et al., J. Exp. Med. 181:1047, 1995; Doolan, D. L. et al., Immunity 7:97, 1997; Bertoni, R. et al., J. Clin. Invest. 100:503, 1997; Threlkeld, S. C. et al., J. Immunol. 159:1648, 1997; Diepolder, H. M. et al., J. Virol. 71:6011, 1997). Accordingly, recall responses are detected by culturing PBL from subjects that have been exposed to the antigen due to disease and thus have generated an immune response “naturally”, or from patients who were vaccinated against the antigen. PBL from subjects are cultured in vitro for 1-2 weeks in the presence of test peptide plus antigen presenting cells (APC) to allow activation of “memory” T cells, as compared to “naive” T cells. At the end of the culture period, T cell activity is detected using assays including ⁵¹Cr release involving peptide-sensitized targets, T cell proliferation, or lymphokine release.

VI.) 108P5H8 Transgenic Animals

Nucleic acids that encode a 108P5H8-related protein can also be used to generate either transgenic animals or “knock out” animals that, in turn, are useful in the development and screening of therapeutically useful reagents. In accordance with established techniques, cDNA encoding 108P5H8 can be used to clone genomic DNA that encodes 108P5H8. The cloned genomic sequences can then be used to generate transgenic animals containing cells that express DNA that encode 108P5H8. Methods for generating transgenic animals, particularly animals such as mice or rats, have become conventional in the art and are described, for example, in U.S. Pat. No. 4,736,866 issued 12 Apr. 1988, and U.S. Pat. No. 4,870,009 issued 26 Sep. 1989. Typically, particular cells would be targeted for 108P5H8 transgene incorporation with tissue-specific enhancers.

Transgenic animals that include a copy of a transgene encoding 108P5H8 can be used to examine the effect of increased expression of DNA that encodes 108P5H8. Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression. In accordance with this aspect of the invention, an animal is treated with a reagent and a reduced incidence of a pathological condition, compared to untreated animals that bear the transgene, would indicate a potential therapeutic intervention for the pathological condition.

Alternatively, non-human homologues of 108P5H8 can be used to construct a 108P5H8 “knock out” animal that has a defective or altered gene encoding 108P5H8 as a result of homologous recombination between the endogenous gene encoding 108P5H8 and altered genomic DNA encoding 108P5H8 introduced into an embryonic cell of the animal. For example, cDNA that encodes 108P5H8 can be used to clone genomic DNA encoding 108P5H8 in accordance with established techniques. A portion of the genomic DNA encoding 108P5H8 can be deleted or replaced with another gene, such as a gene encoding a selectable marker that can be used to monitor integration. Typically, several kilobases of unaltered flanking DNA (both at the 5′ and 3′ ends) are included in the vector (see, e.g., Thomas and Capecchi, Cell, 51:503 (1987) for a description of homologous recombination vectors). The vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected (see, e.g., Li et al., Cell, 69:915 (1992)). The selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras (see, e.g., Bradley, in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-152). A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal, and the embryo brought to term to create a “knock out” animal. Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA. Knock out animals can be characterized, for example, for their ability to defend against certain pathological conditions or for their development of pathological conditions due to absence of a 108P5H8 polypeptide.

VII.) Methods for the Detection of 108P5H8

Another aspect of the present invention relates to methods for detecting 108P5H8 polynucleotides and 108P5H8-related proteins, as well as methods for identifying a cell that expresses 108P5H8. The expression profile of 108P5H8 makes it a diagnostic marker for metastasized disease. Accordingly, the status of 108P5H8 gene products provides information useful for predicting a variety of factors including susceptibility to advanced stage disease, rate of progression, and/or tumor aggressiveness. As discussed in detail herein, the status of 108P5H8 gene products in patient samples can be analyzed by a variety protocols that are well known in the art including immunohistochemical analysis, the variety of Northern blotting techniques including in situ hybridization, RT-PCR analysis (for example on laser capture micro-dissected samples), Western blot analysis and tissue array analysis.

More particularly, the invention provides assays for the detection of 108P5H8 polynucleotides in a biological sample, such as serum, bone, prostate, and other tissues, urine, semen, cell preparations, and the like. Detectable 108P5H8 polynucleotides include, for example, a 108P5H8 gene or fragment thereof, 108P5H8 mRNA, alternative splice variant 108P5H8 mRNAs, and recombinant DNA or RNA molecules that contain a 108P5H8 polynucleotide. A number of methods for amplifying and/or detecting the presence of 108P5H8 polynucleotides are well known in the art and can be employed in the practice of this aspect of the invention.

In one embodiment, a method for detecting an 108P5H8 mRNA in a biological sample comprises producing cDNA from the sample by reverse transcription using at least one primer; amplifying the cDNA so produced using an 108P5H8 polynucleotides as sense and antisense primers to amplify 108P5H8 cDNAs therein; and detecting the presence of the amplified 108P5H8 cDNA. Optionally, the sequence of the amplified 108P5H8 cDNA can be determined.

In another embodiment, a method of detecting a 108P5H8 gene in a biological sample comprises first isolating genomic DNA from the sample; amplifying the isolated genomic DNA using 108P5H8 polynucleotides as sense and antisense primers; and detecting the presence of the amplified 108P5H8 gene. Any number of appropriate sense and antisense probe combinations can be designed from a 192P1E1B nucleotide sequence (see, e.g., FIG. 2) and used for this purpose.

The invention also provides assays for detecting the presence of an 108P5H8 protein in a tissue or other biological sample such as serum, semen, bone, prostate, urine, cell preparations, and the like. Methods for detecting a 108P5H8-related protein are also well known and include, for example, immunoprecipitation, immunohistochemical analysis, Western blot analysis, molecular binding assays, ELISA, ELIFA and the like. For example, a method of detecting the presence of a 108P5H8-related protein in a biological sample comprises first contacting the sample with a 108P5H8 antibody, a 108P5H8-reactive fragment thereof, or a recombinant protein containing an antigen binding region of a 108P5H8 antibody; and then detecting the binding of 108P5H8-related protein in the sample.

Methods for identifying a cell that expresses 108P5H8 are also within the scope of the invention. In one embodiment, an assay for identifying a cell that expresses a 108P5H8 gene comprises detecting the presence of 108P5H8 mRNA in the cell. Methods for the detection of particular mRNAs in cells are well known and include, for example, hybridization assays using complementary DNA probes (such as in situ hybridization using labeled 108P5H8 riboprobes, Northern blot and related techniques) and various nucleic acid amplification assays (such as RT-PCR using complementary primers specific for 108P5H8, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like). Alternatively, an assay for identifying a cell that expresses a 108P5H8 gene comprises detecting the presence of 108P5H8-related protein in the cell or secreted by the cell. Various methods for the detection of proteins are well known in the art and are employed for the detection of 108P5H8-related proteins and cells that express 108P5H8-related proteins.

108P5H8 expression analysis is also useful as a tool for identifying and evaluating agents that modulate 108P5H8 gene expression. For example, 108P5H8 expression is significantly upregulated in prostate cancer, and is expressed in cancers of the tissues listed in Table I. Identification of a molecule or biological agent that inhibits 108P5H8 expression or over-expression in cancer cells is of therapeutic value. For example, such an agent can be identified by using a screen that quantifies 108P5H8 expression by RT-PCR, nucleic acid hybridization or antibody binding.

VIII.) Methods for Monitoring the Status of 108P5H8-Related Genes and Their Products

Oncogenesis is known to be a multistep process where cellular growth becomes progressively dysregulated and cells progress from a normal physiological state to precancerous and then cancerous states (see, e.g., Alers et al., Lab Invest. 77(5): 437-438 (1997) and Isaacs et al., Cancer Surv. 23: 19-32 (1995)). In this context, examining a biological sample for evidence of dysregulated cell growth (such as aberrant 108P5H8 expression in cancers) allows for early detection of such aberrant physiology, before a pathologic state such as cancer has progressed to a stage that therapeutic options are more limited and or the prognosis is worse. In such examinations, the status of 108P5H8 in a biological sample of interest can be compared, for example, to the status of 108P5H8 in a corresponding normal sample (e.g. a sample from that individual or alternatively another individual that is not affected by a pathology). An alteration in the status of 108P5H8 in the biological sample (as compared to the normal sample) provides evidence of dysregulated cellular growth. In addition to using a biological sample that is not affected by a pathology as a normal sample, one can also use a predetermined normative value such as a predetermined normal level of mRNA expression (see, e.g., Grever et al., J. Comp. Neurol. 9 Dec. 1996; 376(2): 306-14 and U.S. Pat. No. 5,837,501) to compare 108P5H8 status in a sample.

The term “status” in this context is used according to its art accepted meaning and refers to the condition or state of a gene and its products. Typically, skilled artisans use a number of parameters to evaluate the condition or state of a gene and its products. These include, but are not limited to the location of expressed gene products (including the location of 108P5H8 expressing cells) as well as the level, and biological activity of expressed gene products (such as 108P5H8 mRNA, polynucleotides and polypeptides). Typically, an alteration in the status of 108P5H8 comprises a change in the location of 108P5H8 and/or 108P5H8 expressing cells and/or an increase in 108P5H8 mRNA and/or protein expression.

108P5H8 status in a sample can be analyzed by a number of means well known in the art, including without limitation, immunohistochemical analysis, in situ hybridization, RT-PCR analysis on laser capture micro-dissected samples, Western blot analysis, and tissue array analysis. Typical protocols for evaluating the status of a 108P5H8 gene and gene products are found, for example in Ausubel et al. eds., 1995, Current Protocols In Molecular Biology, Units 2 (Northern Blotting), 4 (Southern Blotting), 15 (Immunoblotting) and 18 (PCR Analysis). Thus, the status of 108P5H8 in a biological sample is evaluated by various methods utilized by skilled artisans including, but not limited to genomic Southern analysis (to examine, for example perturbations in a 108P5H8 gene), Northern analysis and/or PCR analysis of 108P5H8 mRNA (to examine, for example alterations in the polynucleotide sequences or expression levels of 108P5H8 mRNAs), and, Western and/or immunohistochemical analysis (to examine, for example alterations in polypeptide sequences, alterations in polypeptide localization within a sample, alterations in expression levels of 108P5H8 proteins and/or associations of 108P5H8 proteins with polypeptide binding partners). Detectable 108P5H8 polynucleotides include, for example, a 108P5H8 gene or fragment thereof, 108P5H8 mRNA, alternative splice variants, 108P5H8 mRNAs, and recombinant DNA or RNA molecules containing a 108P5H8 polynucleotide.

The expression profile of 108P5H8 makes it a diagnostic marker for local and/or metastasized disease, and provides information on the growth or oncogenic potential of a biological sample. In particular, the status of 108P5H8 provides information useful for predicting susceptibility to particular disease stages, progression, and/or tumor aggressiveness. The invention provides methods and assays for determining 108P5H8 status and diagnosing cancers that express 108P5H8, such as cancers of the tissues listed in Table I. For example, because 108P5H8 mRNA is so highly expressed in prostate and other cancers relative to normal prostate tissue, assays that evaluate the levels of 108P5H8 mRNA transcripts or proteins in a biological sample can be used to diagnose a disease associated with 108P5H8 dysregulation, and can provide prognostic information useful in defining appropriate therapeutic options.

The expression status of 108P5H8 provides information including the presence, stage and location of dysplastic, precancerous and cancerous cells, predicting susceptibility to various stages of disease, and/or for gauging tumor aggressiveness. Moreover, the expression profile makes it useful as an imaging reagent for metastasized disease. Consequently, an aspect of the invention is directed to the various molecular prognostic and diagnostic methods for examining the status of 108P5H8 in biological samples such as those from individuals suffering from, or suspected of suffering from a pathology characterized by dysregulated cellular growth, such as cancer.

As described above, the status of 108P5H8 in a biological sample can be examined by a number of well-known procedures in the art. For example, the status of 108P5H8 in a biological sample taken from a specific location in the body can be examined by evaluating the sample for the presence or absence of 108P5H8 expressing cells (e.g. those that express 108P5H8 mRNAs or proteins): This examination can provide evidence of dysregulated cellular growth, for example, when 108P5H8-expressing cells are found in a biological sample that does not normally contain such cells (such as a lymph node), because such alterations in the status of 108P5H8 in a biological sample are often associated with dysregulated cellular growth. Specifically, one indicator of dysregulated cellular growth is the metastases of cancer cells from an organ of origin (such as the prostate) to a different area of the body (such as a lymph node). In this context, evidence of dysregulated cellular growth is important for example because occult lymph node metastases can be detected in a substantial proportion of patients with prostate cancer, and such metastases are associated with known predictors of disease progression (see, e.g., Murphy et al., Prostate 42(4): 315-317 (2000);Su et al., Semin. Surg. Oncol. 18(1): 17-28 (2000) and Freeman et al., J Urol 1995 August 154(2 Pt 1):474-8).

In one aspect, the invention provides methods for monitoring 108P5H8 gene products by determining the status of 108P5H8 gene products expressed by cells from an individual suspected of having a disease associated with dysregulated cell growth (such as hyperplasia or cancer) and then comparing the status so determined to the status of 108P5H8 gene products in a corresponding normal sample. The presence of aberrant 108P5H8 gene products in the test sample relative to the normal sample provides an indication of the presence of dysregulated cell growth within the cells of the individual.

In another aspect, the invention provides assays useful in determining the presence of cancer in an individual, comprising detecting a significant increase in 108P5H8 mRNA or protein expression in a test cell or tissue sample relative to expression levels in the corresponding normal cell or tissue. The presence of 108P5H8 mRNA can, for example, be evaluated in tissue samples including but not limited to those listed in Table I. The presence of significant 108P5H8 expression in any of these tissues is useful to indicate the emergence, presence and/or severity of a cancer, since the corresponding normal tissues do not express 108P5H8 mRNA or express it at lower levels.

In a related embodiment, 108P5H8 status is determined at the protein level rather than at the nucleic acid level. For example, such a method comprises determining the level of 108P5H8 protein expressed by cells in a test tissue sample and comparing the level so determined to the level of 108P5H8 expressed in a corresponding normal sample. In one embodiment, the presence of 108P5H8 protein is evaluated, for example, using immunohistochemical methods. 108P5H8 antibodies or binding partners capable of detecting 108P5H8 protein expression are used in a variety of assay formats well known in the art for this purpose.

In a further embodiment, one can evaluate the status of 108P5H8 nucleotide and amino acid sequences in a biological sample in order to identify perturbations in the structure of these molecules. These perturbations can include insertions, deletions, substitutions and the like. Such evaluations are useful because perturbations in the nucleotide and amino acid sequences are observed in a large number of proteins associated with a growth dysregulated phenotype (see, e.g., Marrogi et al., 1999, J. Cutan. Pathol. 26(8):369-378). For example, a mutation in the sequence of 108P5H8 may be indicative of the presence or promotion of a tumor. Such assays therefore have diagnostic and predictive value where a mutation in 108P5H8 indicates a potential loss of function or increase in tumor growth.

A wide variety of assays for observing perturbations in nucleotide and amino acid sequences are well known in the art. For example, the size and structure of nucleic acid or amino acid sequences of 108P5H8 gene products are observed by the Northern, Southern, Western, PCR and DNA sequencing protocols discussed herein. In addition, other methods for observing perturbations in nucleotide and amino acid sequences such as single strand conformation polymorphism analysis are well known in the art (see, e.g., U.S. Pat. No. 5,382,510 issued 7 Sep. 1999, and U.S. Pat.No. 5,952,170 issued 17 Jan. 1995).

Additionally, one can examine the methylation status of a 108P5H8 gene in a biological sample. Aberrant demethylation and/or hypermethylation of CpG islands in gene 5′ regulatory regions frequently occurs in immortalized and transformed cells, and can result in altered expression of various genes. For example, promoter hypermethylation of the pi-class glutathione S-transferase (a protein expressed in normal prostate but not expressed in >90% of prostate carcinomas) appears to permanently silence transcription of this gene and is the most frequently detected genomic alteration in prostate carcinomas (De Marzo et al., Am. J. Pathol. 155(6): 1985-1992 (1999)). In addition, this alteration is present in at least 70% of cases of high-grade prostatic intraepithelial neoplasia (PIN) (Brooks et al., Cancer Epidemiol. Biomarkers Prev., 1998, 7:531-536). In another example, expression of the LAGE-I tumor specific gene (which is not expressed in normal prostate but is expressed in 25-50% of prostate cancers) is induced by deoxy-azacytidine in lymphoblastoid cells, suggesting that tumoral expression is due to demethylation (Lethe et al., Int. J. Cancer 76(6): 903-908 (1998)). A variety of assays for examining methylation status of a gene are well known in the art. For example, one can utilize, in Southern hybridization approaches, methylation-sensitive restriction enzymes that cannot cleave sequences that contain methylated CpG sites to assess the methylation status of CpG islands. In addition, MSP (methylation specific PCR) can rapidly profile the methylation status of all the CpG sites present in a CpG island of a given gene. This procedure involves initial modification of DNA by sodium bisulfite (which will convert all unmethylated cytosines to uracil) followed by amplification using primers specific for methylated versus unmethylated DNA. Protocols involving methylation interference can also be found for example in Current Protocols In Molecular Biology, Unit 12, Frederick M. Ausubel et al. eds., 1995.

Gene amplification is an additional method for assessing the status of 108P5H8. Gene amplification is measured in a sample directly, for example, by conventional Southern blotting or Northern blotting to quantitate the transcription of mRNA (Thomas, 1980, Proc. Natl. Acad. Sci. USA, 77:5201-5205), dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, antibodies are employed that recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn are labeled and the assay carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.

Biopsied tissue or peripheral blood can be conveniently assayed for the presence of cancer cells using for example, Northern, dot blot or RT-PCR analysis to detect 108P5H8 expression. The presence of RT-PCR amplifiable 108P5H8 mRNA provides an indication of the presence of cancer. RT-PCR assays are well known in the art. RT-PCR detection assays for tumor cells in peripheral blood are currently being evaluated for use in the diagnosis and management of a number of human solid tumors. In the prostate cancer field, these include RT-PCR assays for the detection of cells expressing PSA and PSM (Verkaik et al., 1997, Urol. Res. 25:373-384; Ghossein et al., 1995, J. Clin. Oncol. 13:1195-2000; Heston et al., 1995, Clin. Chem. 41:1687-1688).

A further aspect of the invention is an assessment of the susceptibility that an individual has for developing cancer. In one embodiment, a method for predicting susceptibility to cancer comprises detecting 108P5H8 mRNA or 108P5H8 protein in a tissue sample, its presence indicating susceptibility to cancer, wherein the degree of 108P5H8 mRNA expression correlates to the degree of susceptibility. In a specific embodiment, the presence of 108P5H8 in prostate or other tissue is examined, with the presence of 108P5H8 in the sample providing an indication of prostate cancer susceptibility (or the emergence or existence of a prostate tumor). Similarly, one can evaluate the integrity 108P5H8 nucleotide and amino acid sequences in a biological sample, in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like. The presence of one or more perturbations in 108P5H8 gene products in the sample is an indication of cancer susceptibility (or the emergence or existence of a tumor).

The invention also comprises methods for gauging tumor aggressiveness. In one embodiment, a method for gauging aggressiveness of a tumor comprises determining the level of 108P5H8 mRNA or 108P5H8 protein expressed by tumor cells, comparing the level so determined to the level of 108P5H8 mRNA or 108P5H8 protein expressed in a corresponding normal tissue taken from the same individual or a normal tissue reference sample, wherein the degree of 108P5H8 mRNA or 108P5H8 protein expression in the tumor sample relative to the normal sample indicates the degree of aggressiveness. In a specific embodiment, aggressiveness of a tumor is evaluated by determining the extent to which 108P5H8 is expressed in the tumor cells, with higher expression levels indicating more aggressive tumors. Another embodiment is the evaluation of the integrity of 108P5H8 nucleotide and amino acid sequences in a biological sample, in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like. The presence of one or more perturbations indicates more aggressive tumors.

Another embodiment of the invention is directed to methods for observing the progression of a malignancy in an individual over time. In one embodiment, methods for observing the progression of a malignancy in an individual over time comprise determining the level of 108P5H8 mRNA or 108P5H8 protein expressed by cells in a sample of the tumor, comparing the level so determined to the level of 108P5H8 mRNA or 108P5H8 protein expressed in an equivalent tissue sample taken from the same individual at a different time, wherein the degree of 108P5H8 mRNA or 108P5H8 protein expression in the tumor sample over time provides information on the progression of the cancer. In a specific embodiment, the progression of a cancer is evaluated by determining 108P5H8 expression in the tumor cells over time, where increased expression over time indicates a progression of the cancer. Also, one can evaluate the integrity 108P5H8 nucleotide and amino acid sequences in a biological sample in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like, where the presence of one or more perturbations indicates a progression of the cancer.

The above diagnostic approaches can be combined with any one of a wide variety of prognostic and diagnostic protocols known in the art. For example, another embodiment of the invention is directed to methods for observing a coincidence between the expression of 108P5H8 gene and 108P5H8 gene products (or perturbations in 108P5H8 gene and 108P5H8 gene products) and a factor that is associated with malignancy, as a means for diagnosing and prognosticating the status of a tissue sample. A wide variety of factors associated with malignancy can be utilized, such as the expression of genes associated with malignancy (e.g. PSA, PSCA and PSM expression for prostate cancer etc.) as well as gross cytological observations (see, e.g., Bocking et al., 1984, Anal. Quant. Cytol. 6(2):74-88; Epstein, 1995, Hum. Pathol. 26(2):223-9; Thorson et al., 1998, Mod. Pathol. 11(6):543-51; Baisden et al., 1999, Am. J. Surg. Pathol. 23(8):918-24). Methods for observing a coincidence between the expression of 108P5H8 gene and 108P5H8 gene products (or perturbations in 108P5H8 gene and 108P5H8 gene products) and another factor that is associated with malignancy are useful, for example, because the presence of a set of specific factors that coincide with disease provides information crucial for diagnosing and prognosticating the status of a tissue sample.

In one embodiment, methods for observing a coincidence between the expression of 108P5H8 gene and 108P5H8 gene products (or perturbations in 108P5H8 gene and 108P5H8 gene products) and another factor associated with malignancy entails detecting the overexpression of 108P5H8 mRNA or protein in a tissue sample, detecting the overexpression of PSA mRNA or protein in a tissue sample (or PSCA or PSM expression), and observing a coincidence of 108P5H8 mRNA or protein and PSA mRNA or protein overexpression (or PSCA or PSM expression). In a specific embodiment, the expression of 108P5H8 and PSA mRNA in prostate tissue is examined, where the coincidence of 108P5H8 and PSA mRNA overexpression in the sample indicates the existence of prostate cancer, prostate cancer susceptibility or the emergence or status of a prostate tumor.

Methods for detecting and quantifying the expression of 108P5H8 mRNA or protein are described herein, and standard nucleic acid and protein detection and quantification technologies are well known in the art. Standard methods for the detection and quantification of 108P5H8 mRNA include in situ hybridization using labeled 108P5H8 riboprobes, Northern blot and related techniques using 108P5H8 polynucleotide probes, RT-PCR analysis using primers specific for 108P5H8, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like. In a specific embodiment, semi-quantitative RT-PCR is used to detect and quantify 108P5H8 mRNA expression. Any number of primers capable of amplifying 108P5H8 can be used for this purpose, including but not limited to the various primer sets specifically described herein. In a specific embodiment, polyclonal or monoclonal antibodies specifically reactive with the wild-type 108P5H8 protein can be used in an immunohistochemical assay of biopsied tissue.

IX.) Identification of Molecules that Interact with 108P5H8

The 108P5H8 protein and nucleic acid sequences disclosed herein allow a skilled artisan to identify proteins, small molecules and other agents that interact with 108P5H8, as well as pathways activated by 108P5H8 via any one of a variety of art accepted protocols. For example, one can utilize one of the so-called interaction trap systems (also referred to as the “two-hybrid assay”). In such systems, molecules interact and reconstitute a transcription factor which directs expression of a reporter gene, whereupon the expression of the reporter gene is assayed. Other systems identify protein-protein interactions in vivo through reconstitution of a eukaryotic transcriptional activator, see, e.g., U.S. Pat. No. 5,955,280 issued 21 Sep. 1999, U.S. Pat. No. 5,925,523 issued 20 Jul. 1999, U.S. Pat. No. 5,846,722 issued 8 Dec. 1998 and U.S. Pat. No. 6,004,746 issued 21 Dec. 1999. Algorithms are also available in the art for genome-based predictions of protein function (see, e.g., Marcotte, et al., Nature 402: 4 Nov. 1999, 83-86).

Alternatively one can screen peptide libraries to identify molecules that interact with 108P5H8 protein sequences. In such methods, peptides that bind to 108P5H8 are identified by screening libraries that encode a random or controlled collection of amino acids. Peptides encoded by the libraries are expressed as fusion proteins of bacteriophage coat proteins, the bacteriophage particles are then screened against the 108P5H8 protein(s).

Accordingly, peptides having a wide variety of uses, such as therapeutic, prognostic or diagnostic reagents, are thus identified without any prior information on the structure of the expected ligand or receptor molecule. Typical peptide libraries and screening methods that can be used to identify molecules that interact with 108P5H8 protein sequences are disclosed for example in U.S. Pat. No. 5,723,286 issued 3 Mar. 1998 and U.S.Pat.No. 5,733,731 issued 31 Mar. 1998.

Alternatively, cell lines that express 108P5H8 are used to identify protein-protein interactions mediated by 108P5H8. Such interactions can be examined using immunoprecipitation techniques (see, e.g., Hamilton B. J., et al. Biochem. Biophys. Res. Commun. 1999, 261:646-51). 108P5H8 protein can be immunoprecipitated from 108P5H8-expressing cell lines using anti-108P5H8 antibodies. Alternatively, antibodies against His-tag can be used in a cell line engineered to express fusions of 108P5H8 and a His-tag (vectors mentioned above). The immunoprecipitated complex can be examined for protein association by procedures such as Western blotting, ³⁵S-methionine labeling of proteins, protein microsequencing, silver staining and two-dimensional gel electrophoresis.

Small molecules and ligands that interact with 108P5H8 can be identified through related embodiments of such screening assays. For example, small molecules can be identified that interfere with protein function, including molecules that interfere with 108P5H8's ability to mediate phosphorylation and de-phosphorylation, interaction with DNA or RNA molecules as an indication of regulation of cell cycles, second messenger signaling or tumorigenesis. Similarly, small molecules that modulate 108P5H8-related ion channel, protein pump, or cell communication functions are identified and used to treat patients that have a cancer that expresses 108P5H8 (see, e.g., Hille, B., Ionic Channels of Excitable Membranes 2^(nd) Ed., Sinauer Assoc., Sunderland, Mass., 1992). Moreover, ligands that regulate 108P5H8 function can be identified based on their ability to bind 108P5H8 and activate a reporter construct. Typical methods are discussed for example in U.S. Pat. No. 5,928,868 issued 27 Jul. 1999, and include methods for forming hybrid ligands in which at least one ligand is a small molecule. In an illustrative embodiment, cells engineered to express a fusion protein of 108P5H8 and a DNA-binding protein are used to co-express a fusion protein of a hybrid ligand/small molecule and a cDNA library transcriptional activator protein. The cells further contain a reporter gene, the expression of which is conditioned on the proximity of the first and second fusion proteins to each other, an event that occurs only if the hybrid ligand binds to target sites on both hybrid proteins. Those cells that express the reporter gene are selected and the unknown small molecule or the unknown ligand is identified. This method provides a means of identifying modulators which activate or inhibit 108P5H8.

An embodiment of this invention comprises a method of screening for a molecule that interacts with an 108P5H8 amino acid sequence shown in FIG. 2 or FIG. 3, comprising the steps of contacting a population of molecules with a 108P5H8 amino acid sequence, allowing the population of molecules and the 108P5H8 amino acid sequence to interact under conditions that facilitate an interaction, determining the presence of a molecule that interacts with the 108P5H8 amino acid sequence, and then separating molecules that do not interact with the 108P5H8 amino acid sequence from molecules that do. In a specific embodiment, the method further comprises purifying, characterizing and identifying a molecule that interacts with the 108P5H8 amino acid sequence. The identified molecule can be used to modulate a function performed by 108P5H8. In a preferred embodiment, the 108P5H8 amino acid sequence is contacted with a library of peptides.

X.) Therapeutic Methods and Compositions

The identification of 108P5H8 as a protein that is normally expressed in a restricted set of tissues, but which is also expressed in prostate and other cancers, opens a number of therapeutic approaches to the treatment of such cancers. As contemplated herein, 108P5H8 functions as a transcription factor involved in activating tumor-promoting genes or repressing genes that block tumorigenesis.

Accordingly, therapeutic approaches that inhibit the activity of a 108P5H8 protein are useful for patients suffering from a cancer that expresses 108P5H8. These therapeutic approaches generally fall into two classes. One class comprises various methods for inhibiting the binding or association of a 108P5H8 protein with its binding partner or with other proteins. Another class comprises a variety of methods for inhibiting the transcription of a 108P5H8 gene or translation of 108P5H8 mRNA.

X.A.) Anti-Cancer Vaccines

The invention provides cancer vaccines comprising a 108P5H8-related protein or 108P5H8-related nucleic acid. In view of the expression of 108P5H8, cancer vaccines prevent and/or treat 108P5H8-expressing cancers with minimal or no effects on non-target tissues. The use of a tumor antigen in a vaccine that generates humoral and/or cell-mediated immune responses as anti-cancer therapy is well known in the art and has been employed in prostate cancer using human PSMA and rodent PAP immunogens (Hodge et al., 1995, Int. J. Cancer 63:231-237; Fong et al., 1997, J. Immunol. 159:3113-3117).

Such methods can be readily practiced by employing a 108P5H8-related protein, or an 108P5H8-encoding nucleic acid molecule and recombinant vectors capable of expressing and presenting the 108P5H8 immunogen (which typically comprises a number of antibody or T cell epitopes). Skilled artisans understand that a wide variety of vaccine systems for delivery of immunoreactive epitopes are known in the art (see, e.g., Heryln et al., Ann Med 1999 February 31(1):66-78; Maruyama et al., Cancer Immunol Immunother 2000 June 49(3):123-32) Briefly, such methods of generating an immune response (e.g. humoral and/or cell-mediated) in a mammal, comprise the steps of: exposing the mammal's immune system to an immunoreactive epitope (e.g. an epitope present in a 108P5H8 protein shown in FIG. 3 or analog or homolog thereof) so that the mammal generates an immune response that is specific for that epitope (e.g. generates antibodies that specifically recognize that epitope). In a preferred method, a 108P5H8 immunogen contains a biological motif, see e.g., Tables V-XVIII, XXII, and XXIII, or a peptide of a size range from 108P5H8 indicated in FIG. 5, FIG. 6, FIG. 7, FIG. 8, and FIG. 9.

The entire 108P5H8 protein, immunogenic regions or epitopes thereof can be combined and delivered by various means. Such vaccine compositions can include, for example, lipopeptides (e.g., Vitiello, A. et al., J. Clin. Invest. 95:341, 1995), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge, et al., Molec. Immunol. 28:287-294, 1991: Alonso et al., Vaccine 12:299-306, 1994; Jones et al., Vaccine 13:675-681, 1995), peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et al., Clin Exp Immunol. 113:235-243, 1998), multiple antigen peptide systems (MAPs) (see e.g., Tam, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413, 1988; Tam, J. P., J. Immunol. Methods 196:17-32, 1996), peptides formulated as multivalent peptides; peptides for use in ballistic delivery systems, typically crystallized peptides, viral delivery vectors (Perkus, M. E. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 379, 1996; Chakrabarti, S. et al., Nature 320:535, 1986; Hu, S. L. et al., Nature 320:537, 1986; Kieny, M. -P. et al., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al., J. Infect. Dis. 124:148, 1971; Chanda, P. K. et al., Virology 175:535, 1990), particles of viral or synthetic origin (e.g., Kofler, N. et al., J. Immunol. Methods. 192:25, 1996; Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649, 1995), adjuvants (Warren, H. S., Vogel, F. R., and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K. et al., Vaccine 11:293, 1993), liposomes (Reddy, R. et al., J. Immunol. 148:1585, 1992; Rock, K. L., Immunol. Today 17:131, 1996), or, naked or particle absorbed cDNA (Ulmer, J. B. et al., Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., and Webster, R. G., Vaccine 11:957, 1993; Shiver, J. W. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev. Immunol. 12:923, 1994 and Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993). Toxin-targeted delivery technologies, also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Mass.) may also be used.

In patients with 108P5H8-associated cancer, the vaccine compositions of the invention can also be used in conjunction with other treatments used for cancer, e.g., surgery, chemotherapy, drug therapies, radiation therapies, etc. including use in combination with immune adjuvants such as IL-2, IL-12, GM-CSF, and the like.

Cellular Vaccines:

CTL epitopes can be determined using specific algorithms to identify peptides within 108P5H8 protein that bind corresponding HLA alleles (see e.g., Table IV; Epimer™ and Epimatrix™, Brown University; and, BIMAS,. In a preferred embodiment, a 108P5H8 immunogen contains one or more amino acid sequences identified using techniques well known in the art, such as the sequences shown in Tables V-XVIII, XXII, and XXIII or a peptide of 8, 9, 10 or 11 amino acids specified by an HLA Class I motif/supermotif (e.g., Table IV (A), Table IV (D), or Table IV (E)) and/or a peptide of at least 9 amino acids that comprises an HLA Class II motif/supermotif (e.g., Table IV (B) or Table IV (C)). As is appreciated in the art, the HLA Class I binding groove is essentially closed ended so that peptides of only a particular size range can fit into the groove and be bound, generally HLA Class I epitopes are 8, 9, 10, or 11 amino acids long. In contrast, the HLA Class II binding groove is essentially open ended; therefore a peptide of about 9 or more amino acids can be bound by an HLA Class II molecule. Due to the binding groove differences between HLA Class I and II, HLA Class I motifs are length specific, i.e., position two of a Class I motif is the second amino acid in an amino to carboxyl direction of the peptide. The amino acid positions in a Class II motif are relative only to each other, not the overall peptide, i.e., additional amino acids can be attached to the amino and/or carboxyl termini of a motif-bearing sequence. HLA Class II epitopes are often 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 amino acids long, or longer than 25 amino acids.

Antibody-Based Vaccines

A wide variety of methods for generating an immune response in a mammal are known in the art (for example as the first step in the generation of hybridomas). Methods of generating an immune response in a mammal comprise exposing the mammal's immune system to an immunogenic epitope on a protein (e.g. a 108P5H8 protein) so that an immune response is generated. A typical embodiment consists of a method for generating an immune response to 108P5H8 in a host, by contacting the host with a sufficient amount of at least one 108P5H8 B cell or cytotoxic T-cell epitope or analog thereof; and at least one periodic interval thereafter re-contacting the host with the 108P5H8 B cell or cytotoxic T-cell epitope or analog thereof. A specific embodiment consists of a method of generating an immune response against a 108P5H8-related protein or a man-made multiepitopic peptide comprising: administering 108P5H8 immunogen (e.g. a 108P5H8 protein or a peptide fragment thereof, an 108P5H8 fusion protein or analog etc.) in a vaccine preparation to a human or another mammal. Typically, such vaccine preparations further contain a suitable adjuvant (see, e.g., U.S. Pat. No. 6,146,635) or a universal helper epitope such as a PADRE™ peptide (Epimmune Inc., San Diego, Calif.; see, e.g., Alexander et al., J. Immunol. 2000 164(3); 164(3): 1625-1633; Alexander et al., Immunity 1994 1(9): 751-761 and Alexander et al., Immunol. Res. 1998 18(2): 79-92). An alternative method comprises generating an immune response in an individual against a 108P5H8 immunogen by: administering in vivo to muscle or skin of the individual's body a DNA molecule that comprises a DNA sequence that encodes an 108P5H8 immunogen, the DNA sequence operatively linked to regulatory sequences which control the expression of the DNA sequence; wherein the DNA molecule is taken up by cells, the DNA sequence is expressed in the cells and an immune response is generated against the immunogen (see, e.g., U.S. Pat. No. 5,962,428). Optionally a genetic vaccine facilitator such as anionic lipids; saponins; lectins; estrogenic compounds; hydroxylated lower alkyls; dimethyl sulfoxide; and urea is also administered. In addition, an antiidiotypic antibody can be administered that mimics 108P5H8, in order to generate a response to the target antigen.

Nucleic Acid Vaccines:

Vaccine compositions of the invention include nucleic acid-mediated modalities. DNA or RNA that encode protein(s) of the invention can be administered to a patient. Genetic immunization methods can be employed to generate prophylactic or therapeutic humoral and cellular immune responses directed against cancer cells expressing 108P5H8. Constructs comprising DNA encoding a 108P5H8-related protein/immunogen and appropriate regulatory sequences can be injected directly into muscle or skin of an individual, such that the cells of the muscle or skin take-up the construct and express the encoded 108P5H8 protein/immunogen. Alternatively, a vaccine comprises a 108P5H8-related protein. Expression of the 108P5H8-related protein immunogen results in the generation of prophylactic or therapeutic humoral and cellular immunity against cells that bear a 1 08P5H8 protein. Various prophylactic and therapeutic genetic immunization techniques known in the art can be used. Nucleic acid-based delivery is described, for instance, in Wolff et. al., Science 247:1465 (1990) as well as U.S. Pat. Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720. Examples of DNA-based delivery technologies include “naked DNA”, facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated (“gene gun”) or pressure-mediated delivery (see, e.g., U.S. Pat. No. 5,922,687).

For therapeutic or prophylactic immunization purposes, proteins of the invention can be expressed via viral or bacterial vectors. Various viral gene delivery systems that can be used in the practice of the invention include, but are not limited to, vaccinia, fowlpox, canarypox, adenovirus, influenza, poliovirus, adeno-associated virus, lentivirus, and sindbis virus (see, e.g., Restifo, 1996, Curr. Opin. Immunol. 8:658-663; Tsang et al. J. Natl. Cancer Inst. 87:982-990 (1995)). Non-viral delivery systems can also be employed by introducing naked DNA encoding a 108P5H8-related protein into the patient (e.g., intramuscularly or intradermally) to induce an anti-tumor response.

Vaccinia virus is used, for example, as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into a host, the recombinant vaccinia virus expresses the protein immunogenic peptide, and thereby elicits a host immune response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al., Nature 351:456-460 (1991). A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g. adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein.

Thus, gene delivery systems are used to deliver a 108P5H8-related nucleic acid molecule. In one embodiment, the full-length human 108P5H8 cDNA is employed. In another embodiment, 108P5H8 nucleic acid molecules encoding specific cytotoxic T lymphocyte (CTL) and/or antibody epitopes are employed.

Ex Vivo Vaccines

Various ex vivo strategies can also be employed to generate an immune response. One approach involves the use of antigen presenting cells (APCs) such as dendritic cells (DC) to present 108P5H8 antigen to a patient's immune system. Dendritic cells express MHC class I and II molecules, B7 co-stimulator, and IL-12, and are thus highly specialized antigen presenting cells. In prostate cancer, autologous dendritic cells pulsed with peptides of the prostate-specific membrane antigen (PSMA) are being used in a Phase I clinical trial to stimulate prostate cancer patients' immune systems (Tjoa et al., 1996, Prostate 28:65-69; Murphy et al., 1996, Prostate 29:371-380). Thus, dendritic cells can be used to present 108P5H8 peptides to T cells in the context of MHC class I or II molecules. In one embodiment, autologous dendritic cells are pulsed with 108P5H8 peptides capable of binding to MHC class I and/or class II molecules. In another embodiment, dendritic cells are pulsed with the complete 108P5H8 protein. Yet another embodiment involves engineering the overexpression of a 108P5H8 gene in dendritic cells using various implementing vectors known in the art, such as adenovirus (Arthur et al., 1997, Cancer Gene Ther. 4:17-25), retrovirus (Henderson et al., 1996, Cancer Res. 56:3763-3770), lentivirus, adeno-associated virus, DNA transfection (Ribas et al., 1997, Cancer Res. 57:2865-2869), or tumor-derived RNA transfection (Ashley et al., 1997, J. Exp. Med. 186:1177-1182). Cells that express 108P5H8 can also be engineered to express immune modulators, such as GM-CSF, and used as immunizing agents.

X.B.) 108P5H8 as a Target for Antibody-Based Therapy

108P5H8 is an attractive target for antibody-based therapeutic strategies. A number of antibody strategies are known in the art for targeting both extracellular and intracellular molecules (see, e.g., complement and ADCC mediated killing as well as the use of intrabodies). Because 108P5H8 is expressed by cancer cells of various lineages relative to corresponding normal cells, systemic administration of 108P5H8-immunoreactive compositions are prepared that exhibit excellent sensitivity without toxic, non-specific and/or non-target effects caused by binding of the immunoreactive composition to non-target organs and tissues. Antibodies specifically reactive with domains of 108P5H8 are useful to treat 108P5H8-expressing cancers systemically, either as conjugates with a toxin or therapeutic agent, or as naked antibodies capable of inhibiting cell proliferation or function.

108P5H8 antibodies can be introduced into a patient such that the antibody binds to 108P5H8 and modulates a function, such as an interaction with a binding partner, and consequently mediates destruction of the tumor cells and/or inhibits the growth of the tumor cells. Mechanisms by which such antibodies exert a therapeutic effect can include complement-mediated cytolysis, antibody-dependent cellular cytotoxicity, modulation of the physiological function of 108P5H8, inhibition of ligand binding or signal transduction pathways, modulation of tumor cell differentiation, alteration of tumor angiogenesis factor profiles, and/or apoptosis.

Those skilled in the art understand that antibodies can be used to specifically target and bind immunogenic molecules such as an immunogenic region of a 108P5H8 sequence shown in FIG. 2 or FIG. 3. In addition, skilled artisans understand that it is routine to conjugate antibodies to cytotoxic agents (see, e.g., Slevers et al. Blood 93:11 3678-3684 (Jun. 1, 1999)). When cytotoxic and/or therapeutic agents are delivered directly to cells, such as by conjugating them to antibodies specific for a molecule expressed by that cell (e.g. 108P5H8), the cytotoxic agent will exert its known biological effect (i.e. cytotoxicity) on those cells.

A wide variety of compositions and methods for using antibody-cytotoxic agent conjugates to kill cells are known in the art. In the context of cancers, typical methods entail administering to an animal having a tumor a biologically effective amount of a conjugate comprising a selected cytotoxic and/or therapeutic agent linked to a targeting agent (e.g. an anti-108P5H8 antibody) that binds to a marker (e.g. 108P5H8) expressed, accessible to binding or localized on the cell surfaces. A typical embodiment is a method of delivering a cytotoxic and/or therapeutic agent to a cell expressing 108P5H8, comprising conjugating the cytotoxic agent to an antibody that immunospecifically binds to a 108P5H8 epitope, and, exposing the cell to the antibody-agent conjugate. Another illustrative embodiment is a method of treating an individual suspected of suffering from metastasized cancer, comprising a step of administering parenterally to said individual a pharmaceutical composition comprising a therapeutically effective amount of an antibody conjugated to a cytotoxic and/or therapeutic agent.

Cancer immunotherapy using anti-108P5H8 antibodies can be done in accordance with various approaches that have been successfully employed in the treatment of other types of cancer, including but not limited to colon cancer (Arlen et al., 1998, Crit. Rev. Immunol. 18:133-138), multiple myeloma (Ozaki et al., 1997, Blood 90:3179-3186, Tsunenari et al., 1997, Blood 90:2437-2444), gastric cancer (Kasprzyk et al., 1992, Cancer Res. 52:2771-2776), B-cell lymphoma (Funakoshi et al., 1996, J. Immunother. Emphasis Tumor Immunol. 19:93-101), leukemia (Zhong et al., 1996, Leuk. Res. 20:581-589), colorectal cancer (Moun et al., 1994, Cancer Res. 54:6160-6166; Velders et al., 1995, Cancer Res. 55:4398-4403), and breast cancer (Shepard et al., 1991, J. Clin. Immunol. 11:117-127). Some therapeutic approaches involve conjugation of naked antibody to a toxin or radioisotope, such as the conjugation of Y⁹¹ or I¹³¹ to anti-CD20 antibodies (e.g., Zevalin™, IDEC Pharmaceuticals Corp. or Bexxar™, Coulter Pharmaceuticals), while others involve co-administration of antibodies and other therapeutic agents, such as Herceptin™ (trastuzumab) with paclitaxel (Genentech, Inc.). The antibodies can be conjugated to a therapeutic agent. To treat prostate cancer, for example, 108P5H8 antibodies can be administered in conjunction with radiation, chemotherapy or hormone ablation. Also, antibodies can be conjugated to a toxin such as calicheamicin (e.g., Mylotarg™, Wyeth-Ayerst, Madison, N.J., a recombinant humanized IgG₄ kappa antibody conjugated to antitumor antibiotic calicheamicin) or a maytansinoid (e.g., taxane-based Tumor-Activated Prodrug, TAP, platform, ImmunoGen, Cambridge, Mass., also see e.g., U.S. Pat. No. 5,416,064).

Although 108P5H8 antibody therapy is useful for all stages of cancer, antibody therapy can be particularly appropriate in advanced or metastatic cancers. Treatment with the antibody therapy of the invention is indicated for patients who have received one or more rounds of chemotherapy. Alternatively, antibody therapy of the invention is combined with a chemotherapeutic or radiation regimen for patients who have not received chemotherapeutic treatment. Additionally, antibody therapy can enable the use of reduced dosages of concomitant chemotherapy, particularly for patients who do not tolerate the toxicity of the chemotherapeutic agent very well. Fan et al. (Cancer Res. 53:4637-4642, 1993), Prewett et al. (International J. of Onco. 9:217-224, 1996), and Hancock et al. (Cancer Res. 51:4575-4580, 1991) describe the use of various antibodies together with chemotherapeutic agents.

Although 108P5H8 antibody therapy is useful for all stages of cancer, antibody therapy can be particularly appropriate in advanced or metastatic cancers. Treatment with the antibody therapy of the invention is indicated for patients who have received one or more rounds of chemotherapy. Alternatively, antibody therapy of the invention is combined with a chemotherapeutic or radiation regimen for patients who have not received chemotherapeutic treatment. Additionally, antibody therapy can enable the use of reduced dosages of concomitant chemotherapy, particularly for patients who do not tolerate the toxicity of the chemotherapeutic agent very well.

Cancer patients can be evaluated for the presence and level of 108P5H8 expression, preferably using immunohistochemical assessments of tumor tissue, quantitative 108P5H8 imaging, or other techniques that reliably indicate the presence and degree of 108P5H8 expression. Immunohistochemical analysis of tumor biopsies or surgical specimens is preferred for this purpose. Methods for immunohistochemical analysis of tumor tissues are well known in the art.

Anti-108P5H8 monoclonal antibodies that treat prostate and other cancers include those that initiate a potent immune response against the tumor or those that are directly cytotoxic. In this regard, anti-108P5H8 monoclonal antibodies (mAbs) can elicit tumor cell lysis by either complement-mediated or antibody-dependent cell cytotoxicity (ADCC) mechanisms, both of which require an intact Fc portion of the immunoglobulin molecule for interaction with effector cell Fc receptor sites on complement proteins. In addition, anti-108P5H8 mAbs that exert a direct biological effect on tumor growth are useful to treat cancers that express 108P5H8. Mechanisms by which directly cytotoxic mAbs act include: inhibition of cell growth, modulation of cellular differentiation, modulation of tumor angiogenesis factor profiles, and the induction of apoptosis. The mechanism(s) by which a particular anti-108P5H8 mAb exerts an anti-tumor effect is evaluated using any number of in vitro assays that evaluate cell death such as ADCC, ADMMC, complement-mediated cell lysis, and so forth, as is generally known in the art.

In some patients, the use of murine or other non-human monoclonal antibodies, or human/mouse chimeric mAbs can induce moderate to strong immune responses against the non-human antibody. This can result in clearance of the antibody from circulation and reduced efficacy. In the most severe cases, such an immune response can lead to the extensive formation of immune complexes which, potentially, can cause renal failure. Accordingly, preferred monoclonal antibodies used in the therapeutic methods of the invention are those that are either fully human or humanized and that bind specifically to the target 108P5H8 antigen with high affinity but exhibit low or no antigenicity in the patient.

Therapeutic methods of the invention contemplate the administration of single anti-108P5H8 mAbs as well as combinations, or cocktails, of different mAbs. Such mAb cocktails can have certain advantages inasmuch as they contain mAbs that target different epitopes, exploit different effector mechanisms or combine directly cytotoxic mAbs with mAbs that rely on immune effector functionality. Such mAbs in combination can exhibit synergistic therapeutic effects. In addition, anti-108P5H8 mAbs can be administered concomitantly with other therapeutic modalities, including but not limited to various chemotherapeutic agents, androgen-blockers, immune modulators (e.g., IL-2, GM-CSF), surgery or radiation. The anti-108P5H8 mAbs are administered in their “naked” or unconjugated form, or can have a therapeutic agent(s) conjugated to them.

Anti-108P5H8 antibody formulations are administered via any route capable of delivering the antibodies to a tumor cell. Routes of administration include, but are not limited to, intravenous, intraperitoneal, intramuscular, intratumor, intradermal, and the like. Treatment generally involves repeated administration of the anti-108P5H8 antibody preparation, via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 mg/kg body weight. In general, doses in the range of 10-1000 mg mAb per week are effective and well tolerated.

Based on clinical experience with the Herceptin™ mAb in the treatment of metastatic breast cancer, an initial loading dose of approximately 4 mg/kg patient body weight IV, followed by weekly doses of about 2 mg/kg IV of the anti-108P5H8 mAb preparation represents an acceptable dosing regimen. Preferably, the initial loading dose is administered as a 90 minute or longer infusion. The periodic maintenance dose is administered as a 30 minute or longer infusion, provided the initial dose was well tolerated. As appreciated by those of skill in the art, various factors can influence the ideal dose regimen in a particular case. Such factors include, for example, the binding affinity and half life of the Ab or mAbs used, the degree of 108P5H8 expression in the patient, the extent of circulating shed 108P5H8 antigen, the desired steady-state antibody concentration level, frequency of treatment, and the influence of chemotherapeutic or other agents used in combination with the treatment method of the invention, as well as the health status of a particular patient.

Optionally, patients should be evaluated for the levels of 108P5H8 in a given sample (e.g. the levels of circulating 108P5H8 antigen and/or 108P5H8 expressing cells) in order to assist in the determination of the most effective dosing regimen, etc. Such evaluations are also used for monitoring purposes throughout therapy, and are useful to gauge therapeutic success in combination with the evaluation of other parameters (for example, urine cytology and/or ImmunoCyt levels in bladder cancer therapy, or by analogy, serum PSA levels in prostate cancer therapy).

Anti-idiotypic anti-108P5H8 antibodies can also be used in anti-cancer therapy as a vaccine for inducing an immune response to cells expressing a 108P5H8-related protein. In particular, the generation of anti-idiotypic antibodies is well known in the art; this methodology can readily be adapted to generate anti-idiotypic anti-108P5H8 antibodies that mimic an epitope on a 108P5H8-related protein (see, for example, Wagner et al., 1997, Hybridoma 16: 33-40; Foon et al., 1995, J. Clin. Invest. 96:334-342; Herlyn et al., 1996, Cancer Immunol. Immunother. 43:65-76). Such an anti-idiotypic antibody can be used in cancer vaccine strategies.

X.C.) 108P5H8 as a Target for Cellular Immune Responses

Vaccines and methods of preparing vaccines that contain an immunogenically effective amount of one or more HLA-binding peptides as described herein are further embodiments of the invention. Furthermore, vaccines in accordance with the invention encompass compositions of one or more of the claimed peptides. A peptide can be present in a vaccine individually. Alternatively, the peptide can exist as a homopolymer comprising multiple copies of the same peptide, or as a heteropolymer of various peptides. Polymers have the advantage of increased immunological reaction and, where different peptide epitopes are used to make up the polymer, the additional ability to induce antibodies and/or CTLs that react with different antigenic determinants of the pathogenic organism or tumor-related peptide targeted for an immune response. The composition can be a naturally occurring region of an antigen or can be prepared, e.g., recombinantly or by chemical synthesis.

Carriers that can be used with vaccines of the invention are well known in the art, and include, e.g., thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly L-lysine, poly L-glutamic acid, influenza, hepatitis B virus core protein, and the like. The vaccines can contain a physiologically tolerable (i.e., acceptable) diluent such as water, or saline, preferably phosphate buffered saline. The vaccines also typically include an adjuvant. Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum are examples of materials well known in the art. Additionally, as disclosed herein, CTL responses can be primed by conjugating peptides of the invention to lipids, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P₃CSS). Moreover, an adjuvant such as a synthetic cytosine-phosphorothiolated-guanine-containing (CpG) oligonucleotides has been found to increase CTL responses 10- to 100-fold. (see, e.g. Davila and Celis J. Immunol. 165:539-547 (2000))

Upon immunization with a peptide composition in accordance with the invention, via injection, aerosol, oral, transdermal, transmucosal, intrapleural, intrathecal, or other suitable routes, the immune system of the host responds to the vaccine by producing large amounts of CTLs and/or HTLs specific for the desired antigen. Consequently, the host becomes at least partially immune to later development of cells that express or overexpress 108P5H8 antigen, or derives at least some therapeutic benefit when the antigen was tumor-associated.

In some embodiments, it may be desirable to combine the class I peptide components with components that induce or facilitate neutralizing antibody and or helper T cell responses directed to the target antigen. A preferred embodiment of such a composition comprises class I and class II epitopes in accordance with the invention. An alternative embodiment of such a composition comprises a class I and/or class II epitope in accordance with the invention, along with a cross reactive HTL epitope such as PADRE™ (Epimmune, San Diego, Calif.) molecule (described e.g., in U.S. Pat. No. 5,736,142).

A vaccine of the invention can also include antigen-presenting cells (APC), such as dendritic cells (DC), as a vehicle to present-peptides of the invention. Vaccine compositions can be created in vitro, following dendritic cell mobilization and harvesting, whereby loading of dendritic cells occurs in vitro. For example, dendritic cells are transfected, e.g., with a minigene in accordance with the invention, or are pulsed with peptides. The dendritic cell can then be administered to a patient to elicit immune responses in vivo. Vaccine compositions, either DNA- or peptide-based, can also be administered in vivo in combination with dendritic cell mobilization whereby loading of dendritic cells occurs in vivo.

Preferably, the following principles are utilized when selecting an array of epitopes for inclusion in a polyepitopic composition for use in a vaccine, or for selecting discrete epitopes to be included in a vaccine and/or to be encoded by nucleic acids such as a minigene. It is preferred that each of the following principles be balanced in order to make the selection. The multiple epitopes to be incorporated in a given vaccine composition may be, but need not be, contiguous in sequence in the native antigen from which the epitopes are derived.

1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with tumor clearance. For HLA Class I this includes 3-4 epitopes that come from at least one tumor associated antigen (TAA). For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one TAA (see, e.g., Rosenberg et al., Science 278:1447-1450). Epitopes from one TAA may be used in combination with epitopes from one or more additional TAAs to produce a vaccine that targets tumors with varying expression patterns of frequently-expressed TAAs.

2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC₅₀ of 500 nM or less, often 200 nM or less; and for Class II an IC₅₀ of 1000 nM or less.

3.) Sufficient supermotif bearing-peptides, or a sufficient array of allele-specific motif-bearing peptides, are selected to give broad population coverage. For example, it is preferable to have at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess the breadth, or redundancy of, population coverage.

4.) When selecting epitopes from cancer-related antigens it is often useful to select analogs because the patient may have developed tolerance to the native epitope.

5.) Of particular relevance are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A nested peptide sequence can comprise B cell, HLA class I and/or HLA class II epitopes. When providing nested epitopes, a general objective is to provide the greatest number of epitopes per sequence. Thus, an aspect is to avoid providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a multi-epitopic sequence, such as a sequence comprising nested epitopes, it is generally important to screen the sequence in order to insure that it does not have pathological or other deleterious biological properties.

6.) If a polyepitopic protein is created, or when creating a minigene, an objective is to generate the smallest peptide that encompasses the epitopes of interest. This principle is similar, if not the same as that employed when selecting a peptide comprising nested epitopes. However, with an artificial polyepitopic peptide, the size minimization objective is balanced against the need to integrate any spacer sequences between epitopes in the polyepitopic protein. Spacer amino acid residues can, for example, be introduced to avoid junctional epitopes (an epitope recognized by the immune system, not present in the target antigen and only created by the man-made juxtaposition of epitopes), or to facilitate cleavage between epitopes and thereby enhance epitope presentation. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that non-native epitope. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.

7.) Where the sequences of multiple variants of the same target protein are present, potential peptide epitopes can also be selected on the basis of their conservancy. For example, a criterion for conservancy may define that the entire sequence of an HLA class I binding peptide or the entire 9 -mer core of a class II binding peptide be conserved in a designated percentage of the sequences-evaluated for a specific protein antigen.

X.C.1. Minigene Vaccines

A number of different approaches are available which allow simultaneous delivery of multiple epitopes. Nucleic acids encoding the peptides of the invention are a particularly useful embodiment of the invention. Epitopes for inclusion in a minigene are preferably selected according to the guidelines set forth in the previous section. A preferred means of administering nucleic acids encoding the peptides of the invention uses minigene constructs encoding a peptide comprising one or multiple epitopes of the invention.

The use of multi-epitope minigenes is described below and in, Ishioka et al., J. Immunol. 162:3915-3925, 1999; An, L. and Whitton, J. L., J. Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol. 157:822, 1996; Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al., Vaccine 16:426, 1998. For example, a multi-epitope DNA plasmid encoding supermotif- and/or motif-beating epitopes derived 108P5H8, the PADRE® universal helper T cell epitope (or multiple HTL epitopes from 108P5H8) and an endoplasmic reticulum-translocating signal sequence can be engineered. A vaccine may also comprise epitopes that are derived from other TAAs.

The immunogenicity of a multi-epitopic minigene can be confirmed in transgenic mice to evaluate the magnitude of CTL induction responses against the epitopes tested. Further, the immunogenicity of DNA-encoded epitopes in vivo can be correlated with the in vitro responses of specific CTL lines against target cells transfected with the DNA plasmid. Thus, these experiments can show that the minigene serves to both: 1.) generate a CTL response and 2.) that the induced CTLs recognized cells expressing the encoded epitopes.

For example, to create a DNA sequence encoding the selected epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes may be reverse translated. A human codon usage table can be used to guide the codon choice for each amino acid. These epitope-encoding DNA sequences may be directly adjoined, so that when translated, a continuous polypeptide sequence is created. To optimize expression and/or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequences that can be reverse translated and included in the minigene sequence include: HLA class I epitopes, HLA class II epitopes, antibody epitopes, a ubiquitination signal sequence, and/or an endoplasmic reticulum targeting signal. In addition, HLA presentation of CTL and HTL epitopes may be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL or HTL epitopes; these larger peptides comprising the epitope(s) are within the scope of the invention.

The minigene sequence may be converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30-100 bases long) may be synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques. The ends of the oligonucleotides can be joined, for example, using T4 DNA ligase. This synthetic minigene, encoding the epitope polypeptide, can then be cloned into a desired expression vector.

Standard regulatory sequences well known to those of skill in the art are preferably included in the vector to ensure expression in the target cells. Several vector elements are desirable: a promoter with a down-stream cloning site for minigene insertion; a polyadenylation signal for efficient transcription termination; an E. coli origin of replication; and an E. coli selectable marker (e.g. ampicillin or kanamycin resistance). Numerous promoters can be used for this purpose, e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat. Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.

Additional vector modifications may be desired to optimize minigene expression and immunogenicity. In some cases, introns are required for efficient gene expression, and one or more synthetic or naturally-occurring introns could be incorporated into the transcribed region of the minigene. The inclusion of mRNA stabilization sequences and sequences for replication in mammalian cells may also be considered for increasing minigene expression.

Once an expression vector is selected, the minigene is cloned into the polylinker region downstream of the promoter. This plasmid is transformed into an appropriate E. coli strain, and DNA is prepared using standard techniques. The orientation and DNA sequence of the minigene, as well as all other elements included in the vector, are confirmed using restriction mapping and DNA sequence analysis. Bacterial cells harboring the correct plasmid can be stored as a master cell bank and a working cell bank.

In addition, immunostimulatory sequences (ISSs or CpGs) appear to play a role in the immunogenicity of DNA vaccines. These sequences may be included in the vector, outside the minigene coding sequence, if desired to enhance immunogenicity.

In some embodiments, a bi-cistronic expression vector which allows production of both the minigene-encoded epitopes and a second protein (included to enhance or decrease immunogenicity) can be used. Examples of proteins or polypeptides that could beneficially enhance the immune response if co-expressed include cytokines (e.g., IL-2, IL-12, GM-CSF), cytokine-inducing molecules (e.g., LeIF), costimulatory molecules, or for HTL responses, pan-DR binding proteins (PADRE™, Epimmune, San Diego, Calif.). Helper (HTL) epitopes can be joined to intracellular targeting signals and expressed separately from expressed CTL epitopes; this allows direction of the HTL epitopes to a cell compartment different than that of the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the HLA class II pathway, thereby improving HTL induction. In contrast to HTL or CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-β) may be beneficial in certain diseases.

Therapeutic quantities of plasmid DNA can be produced for example, by fermentation in E. coli, followed by purification. Aliquots from the working cell bank are used to inoculate growth medium, and grown to saturation in shaker flasks or a bioreactor according to well-known techniques. Plasmid DNA can be purified using standard bioseparation technologies such as solid phase anion-exchange resins supplied by QIAGEN, Inc. (Valencia, Calif.). If required, supercoiled DNA can be isolated from the open circular and linear forms using gel electrophoresis or other methods.

Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate-buffer saline (PBS). This approach, known as “naked DNA,” is currently being used for intramuscular (IM) administration in clinical trials. To maximize the immunotherapeutic effects of minigene DNA vaccines, an alternative method for formulating purified plasmid DNA may be desirable. A variety of methods have been described, and new techniques may become available. Cationic lipids, glycolipids, and fusogenic liposomes can also be used in the formulation (see, e.g:, as described by WO 93/24640; Mannino & Gould-Fogerite, BioTechniques 6(7): 682 (1988); U.S. Pat No. 5,279,833; WO 91/06309; and Felgner, et al., Proc. Nat'l Acad. Sci. USA 84:7413 (1987). In addition, peptides and compounds referred to collectively as protective, interactive, non-condensing compounds (PINC) could also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types.

Target cell sensitization can be used as a functional assay for expression and HLA class I presentation of minigene-encoded CTL epitopes. For example, the plasmid DNA is introduced into a mammalian cell line that is suitable as a target for standard CTL chromium release assays. The transfection method used will be dependent on the final formulation. Electroporation can be used for “naked” DNA, whereas cationic lipids allow direct in vitro transfection. A plasmid expressing green fluorescent protein (GFP) can be co-transfected to allow enrichment of transfected cells using fluorescence activated cell sorting (FACS). These cells are then chromium-51 (⁵¹Cr) labeled and used as target cells for epitope-specific CTL lines; cytolysis, detected by ⁵¹Cr release, indicates both production of, and HLA presentation of, minigene-encoded CTL epitopes. Expression of HTL epitopes may be evaluated in an analogous manner using assays to assess HTL activity.

In vivo immunogenicity is a second approach for functional testing of minigene DNA formulations. Transgenic mice expressing appropriate human HLA proteins are immunized with the DNA product. The dose and route of administration are formulation dependent (e.g., IM for DNA in PBS, intraperitoneal (i.p.) for lipid-complexed DNA). Twenty-one days after immunization, splenocytes are harvested and restimulated for one week in the presence of peptides encoding each epitope being tested. Thereafter, for CTL effector cells, assays are conducted for cytolysis of peptide-loaded, ⁵¹Cr-labeled target cells using standard techniques. Lysis of target cells that were sensitized by HLA loaded with peptide epitopes, corresponding to minigene-encoded epitopes, demonstrates DNA vaccine function for in vivo induction of CTLs. Immunogenicity of HTL epitopes is confirmed in transgenic mice in an analogous manner.

Alternatively, the nucleic acids can be administered using ballistic delivery as described, for instance, in U.S. Pat. No. 5,204,253. Using this technique, particles comprised solely of DNA are administered. In a further alternative embodiment, DNA can be adhered to particles, such as gold particles.

Minigenes can also be delivered using other bacterial or viral delivery systems well known in the art, e.g., an expression construct encoding epitopes of the invention can be incorporated into a viral vector such as vaccinia.

X.C.2. Combinations of CTL Peptides with Helper Peptides

Vaccine compositions comprising CTL peptides of the invention can be modified, e.g., analoged, to provide desired attributes, such as improved serum half life, broadened population coverage or enhanced immunogenicity.

For instance, the ability of a peptide to induce CTL activity can be enhanced by linking the peptide to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. Although a CTL peptide can be directly-linked to a T helper peptide, often CTL epitope/HTL epitope conjugates are linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus may be a hetero- or homo-oligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues and sometimes 10 or more residues. The CTL peptide epitope can be linked to the T helper peptide epitope either directly or via a spacer either at the amino or carboxy terminus of the CTL peptide. The amino terminus of either the immunogenic peptide or the T helper peptide may be acylated.

In certain embodiments, the T helper peptide is one that is recognized by T helper cells present in a majority of a genetically diverse population. This can be accomplished by selecting peptides that bind to many, most, or all of the HLA class II molecules. Examples of such amino acid bind many HLA Class II molecules include sequences from antigens such as tetanus toxoid at positions 830-843 (QYIKANSKFIGITE; SEQ ID NO: 2582), Plasmodium falciparum circumsporozoite (CS) protein at positions 378-398 (DIEKKIAKMEKASSVFNVVNS; SEQ ID NO: 2583), and Streptococcus 18 kD protein at positions 116-131 (GAVDSILGGVATYGAA; SEQ ID NO: 2584). Other examples include peptides bearing a DR 1-4-7 supermotif, or either of the DR3 motifs.

Alternatively, it is possible to prepare synthetic peptides capable of stimulating T helper lymphocytes, in a loosely HLA-restricted fashion, using amino acid sequences not found in nature (see, e.g., PCT publication WO 95/07707). These synthetic compounds called Pan-DR-binding epitopes (e.g., PADRE™, Epimmune, Inc., San Diego, Calif.) are designed to most preferably bind most HLA-DR (human HLA class II) molecules. For instance, a pan-DR-binding epitope peptide having the formula: aKXVAAWTLKAAa (SEQ ID NO: 2585), where “X” is either cyclohexylalanine, phenylalanine, or tyrosine, and a is either D-alanine or L-alanine, has been found to bind to most HLA-DR alleles, and to stimulate the response of T helper lymphocytes from most individuals, regardless of their HLA type. An alternative of a pan-DR binding epitope comprises all “L” natural amino acids and can be provided in the form of nucleic acids that encode the epitope.

HTL peptide epitopes can also be modified to alter their biological properties. For example, they can be modified to include D-amino acids to increase their resistance to proteases and thus extend their serum half life, or they can be conjugated to other molecules such as lipids, proteins, carbohydrates, and the like to increase their biological activity. For example, a T helper peptide can be conjugated to one or more palmitic acid chains at either the amino or carboxyl termini.

X.C.3. Combinations of CTL Peptides with T Cell Priming Agents

In some embodiments it may be desirable to include in the pharmaceutical compositions of the invention at least one component which primes B lymphocytes or T lymphocytes. Lipids have been identified as agents capable of priming CTL in vivo. For example, palmitic acid residues can be attached to the ε-and α-amino groups of a lysine residue and then linked, e.g., via one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. The lipidated peptide can then be administered either directly in a micelle or particle, incorporated into a liposome, or emulsified in an adjuvant, e.g., incomplete Freund's adjuvant. In a preferred embodiment, a particularly effective immunogenic composition comprises palmitic acid attached to ε- and α-amino groups of Lys, which is attached via linkage, e.g., Ser-Ser, to the amino terminus of the immunogenic peptide.

As another example of lipid priming of CTL responses, E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P₃CSS) can be used to prime virus specific CTL when covalently attached to an appropriate peptide (see, e.g., Deres, et al., Nature 342:561, 1989). Peptides of the invention can be coupled to P₃CSS, for example, and the lipopeptide administered to an individual to specifically prime an immune response to the target antigen. Moreover, because the induction of neutralizing antibodies can also be primed with P₃CSS-conjugated epitopes, two such compositions can be combined to more effectively elicit both humoral and cell-mediated responses.

X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL and/or HTL Peptides

An embodiment of a vaccine composition in accordance with the invention comprises ex vivo administration of a cocktail of epitope-bearing peptides to PBMC, or isolated DC therefrom, from the patient's blood. A pharmaceutical to facilitate harvesting of DC can be used, such as Progenipoietin™ (Pharmacia-Monsanto, St. Louis, Mo.) or GM-CSF/IL-4. After pulsing the DC with peptides and prior to reinfusion into patients, the DC are washed to remove unbound peptides. In this embodiment, a vaccine comprises peptide-pulsed DCs which present the pulsed peptide epitopes complexed with HLA molecules on their surfaces.

The DC can be pulsed ex vivo with a cocktail of peptides, some of which stimulate CTL responses to 108P5H8. Optionally, a helper T cell (HTL) peptide, such as a natural or artificial loosely restricted HLA Class II peptide, can be included to facilitate the CTL response. Thus, a vaccine in accordance with the invention is used to treat a cancer which expresses or overexpresses 108P5H8.

X.D. Adoptive Immunotherapy

Antigenic 108P5H8-related peptides are used to elicit a CTL and/or HTL response ex vivo, as well. The resulting CTL or HTL cells, can be used to treat tumors in patients that do not respond to other conventional forms of therapy, or will not respond to a therapeutic vaccine peptide or nucleic acid in accordance with the invention. Ex vivo CTL or HTL responses to a particular antigen are induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptide. After an appropriate incubation time (typically about 7-28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cell (e.g., a tumor cell). Transfected dendritic cells may also be used as antigen presenting cells.

X.E. Administration of Vaccines for Therapeutic or Prophylactic Purposes

Pharmaceutical and vaccine compositions of the invention are typically used to treat and/or prevent a cancer that expresses or overexpresses 108P5H8. In therapeutic applications, peptide and/or nucleic acid compositions are administered to a patient in an amount sufficient to elicit an effective B cell, CTL and/or HTL response to the antigen and to cure or at least partially arrest or slow symptoms and/or complications. An amount adequate to accomplish this is defined as “therapeutically effective dose.” Amounts effective for this use will depend on, e.g., the particular composition administered, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician.

For pharmaceutical compositions, the immunogenic peptides of the invention, or DNA encoding them, are generally administered to an individual already bearing a tumor that expresses 108P5H8. The peptides or DNA encoding them can be administered individually or as fusions of one or more peptide sequences. Patients can be treated with the immunogenic peptides separately or in conjunction with other treatments, such as surgery, as appropriate.

For therapeutic use, administration should generally begin at the first diagnosis of 108P5H8-associated cancer. This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. The embodiment of the vaccine composition (i.e., including, but not limited to embodiments such as peptide cocktails, polyepitopic polypeptides, minigenes, or TAA-specific CTLs or pulsed dendritic cells) delivered to the patient may vary according to the stage of the disease or the patient's health status. For example, in a patient with a tumor that expresses 108P5H8, a vaccine comprising 108P5H8-specific CTL may be more efficacious in killing tumor cells in patient with advanced disease than alternative embodiments.

It is generally important to provide an amount of the peptide epitope delivered by a mode of administration sufficient to effectively stimulate a cytotoxic T cell response; compositions which stimulate helper T cell responses can also be given in accordance with this embodiment of the invention.

The dosage for an initial therapeutic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1,000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. Boosting dosages of between about 1.0 μg to about 50,000 μg of peptide pursuant to a boosting regimen over weeks to months may be administered depending upon the patient's response and condition as determined by measuring the specific activity of CTL and HTL obtained from the patient's blood. Administration should continue until at least clinical symptoms or laboratory tests indicate that the neoplasia, has been eliminated or reduced and for a period thereafter. The dosages, routes of administration, and dose schedules are adjusted in accordance with methodologies known in the art.

In certain embodiments, the peptides and compositions of the present invention are employed in serious disease states, that is, life-threatening or potentially life threatening situations. In such cases, as a result of the minimal amounts of extraneous substances and the relative nontoxic nature of the peptides in preferred compositions of the invention, it is possible and may be felt desirable by the treating physician to administer substantial excesses of these peptide compositions relative to these stated dosage amounts.

The vaccine compositions of the invention can also be used purely as prophylactic agents. Generally the dosage for an initial prophylactic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. This is followed by boosting dosages of between about 1.0 μg to about 50,000 μg of peptide administered at defined intervals from about four weeks to six months after the initial administration of vaccine. The immunogenicity of the vaccine can be assessed by measuring the specific activity of CTL and HTL obtained from a sample of the patient's blood.

The pharmaceutical compositions for therapeutic treatment are intended for parenteral, topical, oral, nasal, intrathecal, or local (e.g. as a cream or topical ointment) administration. Preferably, the pharmaceutical compositions are administered parentally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic peptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier.

A variety of aqueous carriers may be used, e.g., water, buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well-known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration.

The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservatives, and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.

The concentration of peptides of the invention in the pharmaceutical formulations can vary widely, i.e., from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.

A human unit dose form of a composition is typically included in a pharmaceutical composition that comprises a human unit dose of an acceptable carrier, in one embodiment an aqueous carrier, and is administered in a volume/quantity that is known-by those of skill in the art to be used for administration of such compositions to humans (see, e.g., Remington's Pharmaceutical Sciences, 17^(th) Edition, A. Gennaro, Editor, Mack Publishing Co., Easton, Pa., 1985). For example a peptide dose for initial immunization can be from about 1 to about 50,000 μg, generally 100-5,000 μg, for a 70 kg patient. For example, for nucleic acids an initial immunization may be performed using an expression vector in the form of naked nucleic acid administered IM (or SC or ID) in the amounts of 0.5-5 mg at multiple sites. The nucleic acid (0.1 to 1000 μg) can also be administered using a gene gun. Following an incubation period of 3-4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-10⁷ to 5×10⁹ pfu.

For antibodies, a treatment generally involves repeated administration of the anti-108P5H8 antibody preparation, via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0.1 to about 10 mg/kg body weight. In general, doses in the range of 10-500 mg mAb per week are effective and well tolerated. Moreover, an initial loading dose of approximately 4 mg/kg patient body weight IV, followed by weekly doses of about 2 mg/kg IV of the anti-108P5H8 mAb preparation represents an acceptable dosing regimen. As appreciated by those of skill in the art, various factors can influence the ideal dose in a particular case. Such factors include, for example, half life of a composition, the binding affinity of an Ab, the immunogenicity of a substance, the degree of 108P5H8 expression in the patient, the extent of circulating shed 108P5H8 antigen, the desired steady-state concentration level, frequency of treatment, and the influence of chemotherapeutic or other agents used in combination with the treatment method of the invention, as well as the health status of a particular patient. Non-limiting preferred human unit doses are, for example, 500 μg-1 mg, 1 mg-50 mg, 50 mg-100 mg, 100 mg-200 mg, 200 mg-300 mg, 400 mg-500 mg, 500 mg-600 mg, 600 mg-700 mg, 700 mg-800 mg, 800 mg-900 mg, 900 mg-1 g, or 1 mg-700 mg. In certain embodiments, the dose is in a range of 2-5 mg/kg body weight, e.g., with follow on weekly doses of 1-3 mg/kg; 0.5 mg, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 mg/kg body weight followed, e.g., in two, three or four weeks by weekly doses; 0.5-10 mg/kg body weight, e.g., followed in two, three or four weeks by weekly doses; 225, 250, 275, 300, 325, 350, 375, 400 mg m² of body area weekly; 1-600 mg m² of body area weekly; 225-400 mg m² of body area weekly; these does can be followed by weekly doses for 2, 3, 4, 5, 6, 7, 8, 9, 19, 11, 12 or more weeks.

In one embodiment, human unit dose forms of polynucleotides comprise a suitable dosage range or effective amount that provides any therapeutic effect. As appreciated by one of ordinary skill in the art a therapeutic effect depends on a number of factors, including the sequence of the polynucleotide, molecular weight of the polynucleotide and route of administration. Dosages are generally selected by the physician or other health care professional in accordance with a variety of parameters known in the art, such as severity of symptoms, history of the patient and the like. Generally, for a polynucleotide of about 20 bases, a dosage range may be selected from, for example, an independently selected lower limit such as about 0.1, 0.25, 0.5, 1, 2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400 or 500 mg/kg up to an independently selected upper limit, greater than the lower limit, of about 60, 80, 100, 200, 300, 400, 500, 750, 1000, 1500, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000 or 10,000 mg/kg. For example, a dose may be about any of the following: 0.1 to 100 mg/kg, 0.1 to 50 mg/kg, 0.1 to 25 mg/kg, 0.1 to 10 mg/kg, 1 to 500 mg/kg, 100 to 400 mg/kg, 200 to 300 mg/kg, 1 to 100 mg/kg, 100 to 200 mg/kg, 300 to 400 mg/kg, 400 to 500 mg/kg, 500 to 1000 mg/kg, 500 to 5000 mg/kg, or 500 to 10,000 mg/kg. Generally, parenteral routes of administration may require higher doses of polynucleotide compared to more direct application to the nucleotide to diseased tissue, as do polynucleotides of increasing length.

In one embodiment, human unit dose forms of T-cells comprise a suitable dosage range or effective amount that provides any therapeutic effect. As appreciated by one of ordinary skill in the art, a therapeutic effect depends on a number of factors. Dosages are generally selected by the physician or other health care professional in accordance with a variety of parameters known in the art, such as severity of symptoms, history of the patient and the like. A dose may be about 10⁴ cells to about 10⁶ cells, about 10⁶ cells to about 10⁸ cells, about 10⁸ to about 10¹¹ cells, or about 10⁸ to about 5×10¹⁰ cells. A dose may also about 10⁶ cells/m² to about 10¹⁰ cells/m², or about 10⁶ cells/m² to about 10⁸ cells/m².

Proteins(s) of the invention, and/or nucleic acids encoding the protein(s), can also be administered via liposomes, which may also serve to: 1) target the proteins(s) to a particular tissue, such as lymphoid tissue; 2) to target selectively to diseases cells; or, 3) to increase the half-life of the peptide composition. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations, the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes either filled or decorated with a desired peptide of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the peptide compositions. Liposomes for use in accordance with the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka, et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.

For targeting cells of the immune system, a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated.

For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 25%-75%.

For aerosol administration, immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are about 0.01%-20% by weight, preferably about 1%-10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from about 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute about 0.1%-20% by weight of the composition, preferably about 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g., lecithin for intranasal delivery.

XI.) Diagnostic and Prognostic Embodiments of 108P5H8.

As disclosed herein, 108P5H8 polynucleotides, polypeptides, reactive cytotoxic T cells (CTL), reactive helper T cells (HTL) and anti-polypeptide antibodies are used in well known diagnostic, prognostic and therapeutic assays that examine conditions associated with dysregulated cell growth such as cancer, in particular the cancers listed in Table I (see, e.g., both its specific pattern of tissue expression as well as its overexpression in certain cancers as described for example in Example 4).

108P5H8 can be analogized to a prostate associated antigen PSA, the archetypal marker that has been used by medical practitioners for years to identify and monitor the presence of prostate cancer (see, e.g., Merrill et al., J. Urol. 163(2): 503-5120 (2000); Polascik et al., J. Urol. August; 162(2):293-306 (1999) and Fortier et al., J. Nat. Cancer Inst. 91(19): 1635-1640(1999)). A variety of other diagnostic markers are also used in similar contexts including p53 and K-ras (see, e.g., Tulchinsky et al., Int J Mol Med July 4, 1999(1):99-102 and Minimoto et al., Cancer Detect Prev 2000;24(1):1-12). Therefore, this disclosure of 108P5H8 polynucleotides and polypeptides (as well as 108P5H8 polynucleotide probes and anti-108P5H8 antibodies used to identify the presence of these molecules) and their properties allows skilled artisans to utilize these molecules in methods that are analogous to those used, for example, in a variety of diagnostic assays directed to examining conditions associated with cancer.

Typical embodiments of diagnostic methods which utilize the 108P5H8 polynucleotides, polypeptides, reactive T cells and antibodies are analogous to those methods from well-established diagnostic assays which employ, e.g., PSA polynucleotides, polypeptides, reactive T cells and antibodies. For example, just as PSA polynucleotides are used as probes (for example in Northern analysis, see, e.g., Sharief et al., Biochem. Mol. Biol. Int. 33(3):567-74(1994)) and primers (for example in PCR analysis, see, e.g., Okegawa et al., J. Urol. 163(4): 1189-1190 (2000)) to observe the presence and/or the level of PSA mRNAs in methods of monitoring PSA overexpression or the metastasis of prostate cancers, the 108P5H8 polynucleotides described herein can be utilized in the same way to detect 108P5H8 overexpression or the metastasis of prostate and other cancers expressing this gene. Alternatively, just as PSA polypeptides are used to generate antibodies specific for PSA which can then be used to observe the presence and/or the level of PSA proteins in methods to monitor PSA protein overexpression (see, e.g., Stephan et al., Urology 55(4):560-3 (2000)) or the metastasis of prostate cells (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3):233-7 (1996)), the 108P5H8 polypeptides described herein can be utilized to generate anitbodies for use in detecting 108P5H8 overexpression or the metastasis of prostate cells and cells of other cancers expressing this gene.

Specifically, because metastases involves the movement of cancer cells from an organ of origin (such as the lung or prostate gland etc.) to a different area of the body (such as a lymph node), assays which examine a biological sample for the presence of cells expressing 108P5H8 polynucleotides and/or polypeptides can be used to provide evidence of metastasis. For example, when a biological sample from tissue that does not normally contain 108P5H8-expressing cells (lymph node) is found to contain 108P5H8-expressing cells such as the 108P5H8 expression seen in LAPC4 and LAPC9, xenografts isolated from lymph node and bone metastasis, respectively, this finding is indicative of metastasis.

Alternatively 108P5H8 polynucleotides and/or polypeptides can be used to provide evidence of cancer, for example, when cells in a biological sample that do not normally express 108P5H8 or express 108P5H8 at a different level are found to express 108P5H8 or have an increased expression of 108P5H8 (see, e.g., the 108P5H8 expression in the cancers listed in Table I and in patient samples etc. shown in the accompanying Figures). In such assays, artisans may further wish to generate supplementary evidence of metastasis by testing the biological sample for the presence of a second tissue restricted marker (in addition to 108P5H8) such as PSA, PSCA etc. (see, e.g.; Alanen et al., Pathol. Res. Pract. 192(3): 233-237 (1996)).

Just as PSA polynucleotide fragments and polynucleotide variants are employed by skilled artisans for use in methods of monitoring PSA, 108P5H8 polynucleotide fragments and polynucleotide variants are used in an analogous manner. In particular, typical PSA polynucleotides used in methods of monitoring PSA are probes or primers which consist of fragments of the PSA cDNA sequence. Illustrating this, primers used to PCR amplify a PSA polynucleotide must include less than the whole PSA sequence to function in the polymerase chain reaction. In the context of such PCR reactions, skilled artisans generally create a variety of different polynucleotide fragments that can be used as primers in order to amplify different portions of a polynucleotide of interest or to optimize amplification reactions (see, e.g., Caetano-Anolles, G. Biotechniques 25(3): 472-476, 478-480 (1998); Robertson et al., Methods Mol. Biol. 98:121-154 (1998)). An additional illustration of the use of such fragments is provided in Example 4, where a 108P5H8 polynucleotide fragment is used as a probe to show the expression of 108P5H8 RNAs in cancer cells. In addition, variant polynucleotide sequences are typically used as primers and probes for the corresponding mRNAs in PCR and Northern analyses (see, e.g., Sawai et al., Fetal Diagn. Ther. 1996 November -December 11(6):407-13 and Current Protocols In Molecular Biology, Volume 2, Unit 2, Frederick M. Ausubel et al. eds., 1995)). Polynucleotide fragments and variants are useful in this context where they are capable of binding to a target polynucleotide sequence (e.g., a 108P5H8 polynucleotide shown in FIG. 2 or variant thereof) under conditions of high stringency.

Furthermore, PSA polypeptides which contain an epitope that can be recognized by an antibody or T cell that specifically binds to that epitope are used in methods of monitoring PSA. 108P5H8 polypeptide fragments and polypeptide analogs or variants can also be used in an analogous manner. This practice of using polypeptide fragments or polypeptide variants to generate antibodies (such as anti-PSA antibodies or T cells) is typical in the art with a wide variety of systems such as fusion proteins being used by practitioners (see, e.g., Current Protocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubel et al. eds., 1995). In this context, each epitope(s) functions to provide the architecture with which an antibody or T cell is reactive. Typically, skilled artisans create a variety of different polypeptide fragments that can be used in order to generate immune responses specific for different portions of a polypeptide of interest (see, e.g., U.S. Pat. No. 5,840,501 and U.S. Pat. No. 5,939,533). For example it may be preferable to utilize a polypeptide comprising one of the 108P5H8 biological motifs discussed herein or a motif-bearing subsequence which is readily identified by one of skill in the art based on motifs available in the art. Polypeptide fragments, variants or analogs are typically useful in this context as long as they comprise an epitope capable of generating an antibody or T cell specific for a target polypeptide sequence (e.g. a 108P5H8 polypeptide shown in FIG. 3).

As shown herein, the 108P5H8 polynucleotides and polypeptides (as well as the 108P5H8 polynucleotide probes and anti-108P5H8 antibodies or T cells used to identify the presence of these molecules) exhibit specific properties that make them useful in diagnosing cancers such as those listed in Table I. Diagnostic assays that measure the presence of 108P5H8 gene products, in order to evaluate the presence or onset of a disease condition described herein, such as prostate cancer, are used to identify patients for preventive measures or further monitoring, as has been done so successfully with PSA. Moreover, these materials satisfy a need in the art for molecules having similar or complementary characteristics to PSA in situations where, for example, a definite diagnosis of metastasis of prostatic origin cannot be made on the basis of a test for PSA alone (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3): 233-237 (1996)), and consequently, materials such as 108P5H8 polynucleotides and polypeptides (as well as the 108P5H8 polynucleotide probes and anti-108P5H8 antibodies used to identify the presence of these molecules) need to be employed to confirm a metastases of prostatic origin.

Finally, in addition to their use in diagnostic assays, the 108P5H8 polynucleotides disclosed herein have a number of other utilities such as their use in the identification of oncogenetic associated chromosomal abnormalities in the chromosomal region to which the 108P5H8 gene maps (see Example 3 below). Moreover, in addition to their use in diagnostic assays, the 108P5H8-related proteins and polynucleotides disclosed herein have other utilities such as their use in the forensic analysis of tissues of unknown origin (see, e.g., Takahama K Forensic Sci Int 28 Jun. 1996;80(1-2): 63-9).

Additionally, 108P5H8-related proteins or polynucleotides of the invention can be used to treat a pathologic condition characterized by the over-expression of 108P5H8. For example, the amino acid or nucleic acid sequence of FIG. 2 or FIG. 3, or fragments of either, can be used to generate an immune response to a 108P5H8 antigen. Antibodies or other molecules that react with 108P5H8 can be used to modulate the function of this molecule, and thereby provide a therapeutic benefit.

XII.) Inhibition of 108P5H8 Protein Function

The invention includes various methods and compositions for inhibiting the binding of 108P5H8 to its binding partner or its association with other protein(s) as well as methods for inhibiting 108P5H8 function.

XII.A.) Inhibition of 108P5H8 with Intracellular Antibodies

In one approach, a recombinant vector that encodes single chain antibodies that specifically bind to 108P5H8 are introduced into 108P5H8 expressing cells via gene transfer technologies. Accordingly, the encoded single chain anti-108P5H8 antibody is expressed intracellularly, binds to 108P5H8 protein, and thereby inhibits its function. Methods for engineering such intracellular single chain antibodies are well known. Such intracellular antibodies, also known as “intrabodies”, are specifically targeted to a particular compartment within the cell, providing control over where the inhibitory activity of the treatment is focused. This technology has been successfully applied in the art (for review, see Richardson and Marasco, 1995, TIBTECH vol. 13). Intrabodies have been shown to virtually eliminate the expression of otherwise abundant cell surface receptors (see, e.g., Richardson et al., 1995, Proc. Natl. Acad. Sci. USA 92: 3137-3141; Beerli et al., 1994, J. Biol. Chem. 289: 23931-23936; Deshane et al., 1994, Gene Ther. 1: 332-337).

Single chain antibodies comprise the variable domains of the heavy and light chain joined by a flexible linker polypeptide, and are expressed as a single polypeptide. Optionally, single chain antibodies are expressed as a single chain variable region fragment joined to the light chain constant region. Well-known intracellular trafficking signals are engineered into recombinant polynucleotide vectors encoding such single chain antibodies in order to precisely target the intrabody to the desired intracellular compartment. For example, intrabodies targeted to the endoplasmic reticulum (ER) are engineered to incorporate a leader peptide and, optionally, a C-terminal ER retention signal, such as the KDEL amino acid motif. Intrabodies intended to exert activity in the nucleus are engineered to include a nuclear localization signal. Lipid moieties are joined to intrabodies in order to tether the intrabody to the cytosolic side of the plasma membrane. Intrabodies can also be targeted to exert function in the cytosol. For example, cytosolic intrabodies are used to sequester factors within the cytosol, thereby preventing them from being transported to their natural cellular destination.

In one embodiment, intrabodies are used to capture 108P5H8 in the nucleus, thereby preventing its activity within the nucleus. Nuclear targeting signals are engineered into such 108P5H8 intrabodies in order to achieve the desired targeting. Such 108P5H8 intrabodies are designed to bind specifically to a particular 108P5H8 domain. In another embodiment, cytosolic intrabodies that specifically bind to a 108P5H8 protein are used to prevent 108P5H8 from gaining access to the nucleus, thereby preventing it from exerting any biological activity within the nucleus (e.g., preventing 108P5H8 from forming transcription complexes with other factors).

In order to specifically direct the expression of such intrabodies to particular cells, the transcription of the intrabody is placed under the regulatory control of an appropriate tumor-specific promoter and/or enhancer. In order to target intrabody expression specifically to prostate, for example, the PSA promoter and/or promoter/enhancer can be utilized (See, for example, U.S. Pat. No. 5,919,652 issued 6 Jul. 1999).

XII.B.) Inhibition of 108P5H8 with Recombinant Proteins

In another approach, recombinant molecules bind to 108P5H8 and thereby inhibit 108P5H8 function. For example, these recombinant molecules prevent or inhibit 108P5H8 from accessing/binding to its binding partner(s) or associating with other protein(s). Such recombinant molecules can, for example, contain the reactive part(s) of a 108P5H8 specific antibody molecule. In a particular embodiment, the 108P5H8 binding domain of a 108P5H8 binding partner is engineered into a dimeric fusion protein, whereby the fusion protein comprises two 108P5H8 ligand binding domains linked to the Fc portion of a human IgG, such as human IgG1. Such IgG portion can contain, for example, the C_(H)2 and C_(H)3 domains and the hinge region, but not the C_(H)1 domain. Such dimeric fusion proteins are administered in soluble form to patients suffering from a cancer associated with the expression of 108P5H8, whereby the dimeric fusion protein specifically binds to 108P5H8 and blocks 108P5H8 interaction with a binding partner. Such dimeric fusion proteins are further combined into multimeric proteins using known antibody linking technologies.

XII.C.) Inhibition of 108P5H8 Transcription or Translation

The present invention also comprises various methods and compositions for inhibiting the transcription of the 108P5H8 gene. Similarly, the invention also provides methods and compositions for inhibiting the translation of 108P5H8 mRNA into protein.

In one approach, a method of inhibiting the transcription of the 108P5H8 gene comprises contacting the 108P5H8 gene with a 108P5H8 antisense polynucleotide. In another approach, a method of inhibiting 108P5H8 mRNA translation comprises contacting a 108P5H8 mRNA with an antisense polynucleotide. In another approach, a 108P5H8 specific ribozyme is used to cleave a 108P5H8 message, thereby inhibiting translation. Such antisense and ribozyme based methods can also be directed to the regulatory regions of the 108P5H8 gene, such as 108P5H8 promoter and/or enhancer elements. Similarly, proteins capable of inhibiting a 108P5H8 gene transcription factor are used to inhibit 108P5H8 mRNA transcription. The various polynucleotides and compositions useful in the aforementioned methods have been described above. The use of antisense and ribozyme molecules to inhibit transcription and translation is well known in the art.

Other factors that inhibit the transcription of 108P5H8 by interfering with 108P5H8 transcriptional activation are also useful to treat cancers expressing 108P5H8. Similarly, factors that interfere with 108P5H8 processing are useful to treat cancers that express 108P5H8. Cancer treatment methods utilizing such factors are also within the scope of the invention.

XII.D.) General Considerations for Therapeutic Strategies

Gene transfer and gene therapy technologies can be used to deliver therapeutic polynucleotide molecules to tumor cells synthesizing 108P5H8 (i.e., antisense, ribozyme, polynucleotides encoding intrabodies and other 108P5H8 inhibitory molecules). A number of gene therapy approaches are known in the art. Recombinant vectors encoding 108P5H8 antisense polynucleotides, ribozymes, factors capable of interfering with 108P5H8 transcription, and so forth, can be delivered to target tumor cells using such gene therapy approaches.

The above therapeutic approaches can be combined with any one of a wide variety of surgical, chemotherapy or radiation therapy regimens. The therapeutic approaches of the invention can enable the use of reduced dosages of chemotherapy (or other therapies) and/or less frequent administration, an advantage for all patients and particularly for those that do not tolerate the toxicity of the chemotherapeutic agent well.

The anti-tumor activity of a particular composition (e.g., antisense, ribozyme, intrabody), or a combination of such compositions, can be evaluated using various in vitro and in vivo assay systems. In vitro assays that evaluate therapeutic activity include cell growth assays, soft agar assays and other assays indicative of tumor promoting activity, binding assays capable of determining the extent to which a therapeutic composition will inhibit the binding of 108P5H8 to a binding partner, etc.

In vivo, the effect of a 108P5H8 therapeutic composition can be evaluated in a suitable animal model. For example, xenogenic prostate cancer models can be used, wherein human prostate cancer explants or passaged xenograft tissues are introduced into immune compromised animals, such as nude or SCID mice (Klein et al., 1997, Nature Medicine 3: 402-408). For example, PCT Patent Application WO98/16628 and U.S. Pat. No. 6,167,540 describe various xenograft models of human prostate cancer capable of recapitulating the development of primary tumors, micrometastasis, and the formation of osteoblastic metastases characteristic of late stage disease. Efficacy can be predicted using assays that measure inhibition of tumor formation, tumor regression or metastasis, and the like.

In vivo assays that evaluate the promotion of apoptosis are useful in evaluating therapeutic compositions. In one embodiment, xenografts from tumor bearing mice treated with the therapeutic composition can be examined for the presence of apoptotic foci and compared to untreated control xenograft-bearing mice. The extent to which apoptotic foci are found in the tumors of the treated mice provides an indication of the therapeutic efficacy of the composition.

The therapeutic compositions used in the practice of the foregoing methods can be formulated into pharmaceutical compositions comprising a carrier suitable for the desired delivery method. Suitable carriers include any material that when combined with the therapeutic composition retains the anti-tumor function of the therapeutic composition and is generally non-reactive with the patient's immune system. Examples include, but are not limited to, any of a number of standard pharmaceutical carriers such as sterile phosphate buffered saline solutions, bacteriostatic water, and the like (see, generally, Remington's Pharmaceutical Sciences 16^(th) Edition, A. Osal., Ed., 1980).

Therapeutic formulations can be solubilized and administered via any route capable of delivering the therapeutic composition to the tumor site. Potentially effective routes of administration include, but are not limited to, intravenous, parenteral, intraperitoneal, intramuscular, intratumor, intradermal, intraorgan, orthotopic, and the like. A preferred formulation for intravenous injection comprises the therapeutic composition in a solution of preserved bacteriostatic water, sterile unpreserved water, and/or diluted in polyvinylchloride or polyethylene bags containing 0.9% sterile Sodium Chloride for Injection, USP. Therapeutic protein preparations can be lyophilized and stored as sterile powders, preferably under vacuum, and then reconstituted in bacteriostatic water (containing for example, benzyl alcohol preservative) or in sterile water prior to injection.

Dosages and administration protocols for the treatment of cancers using the foregoing methods will vary with the method and the target cancer, and will generally depend on a number of other factors appreciated in the art.

XIII.) Kits

For use in the diagnostic and therapeutic applications described herein, kits are also within the scope of the invention. Such kits can comprise a carrier, package or container that is compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the container(s) comprising one of the separate elements to be used in the method. For example, the container(s) can comprise a probe that is or can be detectably labeled. Such probe can be an antibody or polynucleotide specific for a 108P5H8-related protein or a 108P5H8 gene or message, respectively. Where the method utilizes nucleic acid hybridization to detect the target nucleic acid, the kit can also have containers containing nucleotide(s) for amplification of the target nucleic acid sequence and/or a container comprising a reporter-means, such as a biotin-binding protein, such as avidin or streptavidin, bound to a reporter molecule, such as an enzymatic, florescent, or radioisotope label. The kit can include all or part of the amino acid sequence of FIG. 2 or FIG. 3 or analogs thereof, or a nucleic acid molecules that encodes such amino acid sequences.

The kit of the invention will typically comprise the container described above and one or more other containers comprising materials desirable from a commercial and user standpoint, including buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.

A label can be present on the container to indicate that the composition is used for a specific therapy or non-therapeutic application, and can also indicate directions for either in vivo or in vitro use, such as those described above. Directions and or other information can also be included on an insert which is included with the kit.

EXAMPLES

Various aspects of the invention are further described and illustrated by way of the several examples that follow, none of which are intended to limit the scope of the invention.

Example 1 SSH-Generated Isolation of a cDNA Fragment of the 108P5H8 Gene

To isolate genes that are androgen regulated, the androgen-dependent prostate cancer cell line LNCaP was grown in media containing charcoal-stripped serum (steroid hormone depleted) for one week. The cells were subsequently stimulated with 10 nM mibolerone (synthetic androgen) for 9 h and were harvested as a source of mRNA. The 108P5H8 SSH cDNA sequence was derived from a subtraction consisting of LNCaP cells grown in presence of mibolerone minus LNCaP cells grown in absence of mibolerone.

The 108P5H8 SSH cDNA sequence of 448 bp (FIG. 1), showed homology only to ESTs in the dbEST database. The full length 108P5H8 cDNAs and ORFs are described in FIG. 2 with the protein sequences listed in FIG. 3.

Materials and Methods

RNA Isolation:

Tumor tissues were homogenized in Trizol reagent (Life Technologies, Gibco BRL) using 10 ml/g tissue or 10 ml/10⁸ cells to isolate total RNA. Poly A RNA was purified from total RNA using Qiagen's Oligotex mRNA Mini and Midi kits. Total and mRNA were quantified by spectrophotometric analysis (O.D. 260/280 nm) and analyzed by gel electrophoresis.

Oligonucleotides:

The following HPLC purified oligonucleotides were used.

DPNCDN (cDNA synthesis primer): (SEQ ID NO: 2586) 5′TTTTGATCAAGCTT₃₀3′ Adaptor 1: (SEQ ID NO: 2587) 5′CTAATACGACTCACTATAGGGCTCGAGCGGCCGCCCGGGCAG3′ (SEQ ID NO: 2588) 3′GGCCCGTCCTAG5′ Adaptor 2: (SEQ ID NO: 2589) 5′GTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAG3′ (SEQ ID NO: 2590) 3′CGGCTCCTAG5′ PCR primer 1: (SEQ ID NO: 2591) 5′CTAATACGACTCACTATAGGGC3′ Nested primer (NP) 1: (SEQ ID NO: 2592) 5′TCGAGCGGCCGCCCGGGCAGGA3′ Nested primer (NP) 2: (SEQ ID NO: 2593) 5′AGCGTGGTCGCGGCCGAGGA3′

Suppression Subtractive Hybridization:

Suppression Subtractive Hybridization (SSH) was used to identify cDNAs corresponding to genes that are androgen regulated. The SSH reaction utilized cDNA from LNCaP prostate cancer cells grown in presence of mibolerone minus LNCaP cells grown in absence of mibolerone.

The cDNA derived from LNCaP prostate cancer cells grown in absence of mibolerone was used as the source of the “driver” cDNA, while the LNCaP prostate cancer cells grown in presence of mibolerone was used as the source of the “tester” cDNA. Double stranded cDNAs corresponding to tester and driver cDNAs were synthesized from 2 μg of poly(A)⁺ RNA isolated from the relevant tissue, as described above, using CLONTECH's PCR-Select cDNA Subtraction Kit and 1 ng of oligonucleotide DPNCDN as primer. First- and second-strand synthesis were carried out as described in the Kit's user manual protocol (CLONTECH Protocol No. PT1117-1, Catalog No. K1804-1). The resulting cDNA was digested with Dpn II for 3 hrs at 37° C. Digested cDNA was extracted with phenol/chloroform (1:1) and ethanol precipitated.

Tester cDNA was generated by diluting 1 μl of Dpn II digested cDNA from the relevant tissue source (see above) (400 ng) in 5 μl of water. The diluted cDNA (2 μl, 160 ng) was then ligated to 2 μl of Adaptor 1 and Adaptor 2 (10 μM), in separate ligation reactions, in a total volume of 10 μl at 16° C. overnight, using 400 u of T4 DNA ligase (CLONTECH). Ligation was terminated with 1 μl of 0.2 M EDTA and heating at 72° C. for 5 min.

The first hybridization was performed by adding 1.5 μl (600 ng) of driver cDNA to each of two tubes containing 1.5 μl (20 ng) Adaptor 1- and Adaptor 2-ligated tester cDNA. In a final volume of 4 μl, the samples were overlaid with mineral oil, denatured in an MJ Research thermal cycler at 98° C. for 1.5 minutes, and then were allowed to hybridize for 8 hrs at 68° C. The two hybridizations were then mixed together with an additional 1 μl of fresh denatured driver cDNA and were allowed to hybridize overnight at 68° C. The second hybridization was then diluted in 200 μl of 20 mM Hepes, pH 8.3, 50 mM NaCl, 0.2 mM EDTA, heated at 70° C. for 7 min. and stored at −20° C.

PCR Amplification, Cloning and Sequencing of Gene Fragments Generated from SSH:

To amplify gene fragments resulting from SSH reactions, two PCR amplifications were performed. In the primary PCR reaction 1 μl of the diluted final hybridization mix was added to 1 μl of PCR primer 1 (10 μM), 0.5 μl dNTP mix (10 μM), 2.5 μl 10× reaction buffer (CLONTECH) and 0.5 μl 50× Advantage cDNA polymerase Mix (CLONTECH) in a final volume of 25 μl. PCR 1 was conducted using the following conditions: 75° C. for 5 min., 94° C. for 25 sec., then 27 cycles of 94° C. for 10 sec, 66° C. for 30 sec, 72° C. for 1.5 min. Five separate-primary PCR reactions were performed for each experiment. The products were pooled and diluted 1:10 with water. For the secondary PCR reaction, 1 μl from the pooled and diluted primary PCR reaction was added to the same reaction mix as used for PCR 1, except that primers NP1 and NP2 (10 μM) were used instead of PCR primer 1. PCR 2 was performed using 10- 12 cycles of 94° C. for 10 sec, 68° C. for 30 sec, and 72° C. for 1.5 minutes. The PCR products were analyzed using 2% agarose gel electrophoresis.

The PCR products were inserted into pCR2.1 using the T/A vector cloning kit (Invitrogen). Transformed E. coli were subjected to blue/white and ampicillin selection. White colonies were picked and arrayed into 96 well plates and were grown in liquid culture overnight. To identify inserts, PCR amplification was performed on 1 ml of bacterial culture using the conditions of PCR1 and NP1 and NP2 as primers. PCR products were analyzed using 2% agarose gel electrophoresis.

Bacterial clones were stored in 20% glycerol in a 96 well format. Plasmid DNA was prepared, sequenced, and subjected to nucleic acid homology searches of the GenBank, dbest, and NCI-CGAP databases.

RT-PCR Expression Analysis:

First strand cDNAs can be generated from 1 μg of mRNA with oligo (dT)12-18 priming using the Gibco-BRL Superscript Preamplification system. The manufacturer's protocol was used which included an incubation for 50 min at 42° C. with reverse transcriptase followed by RNAse H treatment at 37° C. for 20 min. After completing the reaction, the volume can be increased to 200 μl with water prior to normalization. First strand cDNAs from 16 different normal human tissues can be obtained from Clontech.

Normalization of the first strand cDNAs from multiple tissues was performed by using the primers 5′-atatcgccgcgctcgtcgtcgacaa-3′ (SEQ ID NO: 2594) and 5′-agccacacgcagctcattgtagaagg-3′ (SEQ ID NO: 2595) to amplify β-actin. First strand cDNA (5 μl) were amplified in a total volume of 50 μl containing 0.4 μM primers, 0.2 μM each dNTPs, 1×PCR buffer (Clontech, 10 mM Tris-HCL, 1.5 mM MgCl₂, 50 mM KCl, pH8.3) and 1× Klentaq DNA polymerase (Clontech). Five μl of the PCR reaction can be removed at 18, 20, and 22 cycles and used for agarose gel electrophoresis. PCR was performed using an MJ Research thermal cycler under the following conditions: Initial denaturation can be at 94° C. for 15 sec, followed by a 18, 20, and 22 cycles of 94° C. for 15, 65° C. for 2 min, 72° C. for 5 sec. A final extension at 72° C. was carried out for 2 min. After agarose gel electrophoresis, the band intensities of the 283 bp β-actin bands from multiple tissues were compared by visual inspection. Dilution factors for the first strand cDNAs were calculated to result in equal β-actin band intensities in all tissues after 22 cycles of PCR. Three rounds of normalization can be required to achieve equal band intensities in all tissues after 22 cycles of PCR.

To determine expression levels of the 108P5H8 gene, 5 μl of normalized first strand cDNA were analyzed by PCR using 26, and 30 cycles of amplification. Semi-quantitative expression analysis can be achieved by comparing the PCR products at cycle numbers that give light band intensities.

A typical RT-PCR expression analysis is shown in FIG. 10. RT-PCR expression analysis was performed on first strand cDNAs generated using pools of tissues from multiple samples. The cDNAs were shown to be normalized using beta-actin PCR. Strong expression of 108P5H8 was observed in prostate cancer xenograft pool, prostate cancer pool and in the 2 different prostate cancer metastasis samples. Lower expression was detected in bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, ovary cancer pool, breast cancer pool, metastasis pool, pancreas cancer pool, VP1 and VP2.

Example 2 Full Length Cloning of 108P5H8

To isolate genes that are androgen regulated, the androgen-dependent prostate cancer cell line LNCaP was grown in media containing 2% charcoal-stripped serum (steroid hormone depleted) for one week. The cells were then stimulated with 10 nM Mibolerone (synthetic androgen) for 9 hours and were harvested for RNA.

The gene 108P5H8 was derived from an experiment where cDNA derived from LNCaP cells that was androgen-deprived (by growing in the presence of charcoal-stripped serum) was subtracted from cDNA derived from LNCaP cells that were stimulated with mibolerone for 9 hours. The SSH DNA sequence of 448 bp (FIG. 1) is novel and only exhibited homology to human EST sequences in the dbest database.

A full length 108P5H8 cDNA clone (108P5H8 v.1) of 2364 base pairs (bp) was cloned from a prostate library (Lambda ZAP Express, Stratagene) (FIG. 2). The cDNA encodes a putative open reading frame (ORF) of 429 amino acids.

108P5H8 variant 2 and variant 3 were identified. The nucleic acid and protein sequences of all 3 variants are presented in FIG. 3 and FIG. 4. The alignments of all 3 108P5H8 variants are presented in FIG. 4. The nucleic acid sequences of variants 1 and 2 encode identical protein. 108P5H8 v.3 has a base pair variation with a C at position 342 of v.1 converted into G in v.3. This nucleotide change converted amino acid position 30 from aspartic acid in the 108P5H8 v.1 and v.2 protein sequence, to glutamic acid in 108P5H8 v.3.

Analysis of 108P5H8 protein sequence using the PSORT program (http://psort.nibb.acjp:8800/form.html) reveals 6 predicted transmembrane domains. Sequence analysis of 108P5H8 reveals homology to the human zinc transporter protein ZnT4 (Huang and Gitschier, 1997, Nature Genetics 17:292). The 108P5H8 v.1 sequence includes novel 5′ UTR and 3′ UTR sequences, and the molecule contains 75% GC sequence, indicating possible translational regulatory sites.

To further confirm the parameters of a variant, a variety of techniques are available in the art, such as full-length cloning, proteomic validation, PCR-based validation, and 5′ RACE validation, etc. (see e.g., Proteomic Validation: Brennan, S. O., et al., Albumin banks peninsula: a new termination variant characterized by electrospray mass spectrometry, Biochem Biophys Acta. 1999 Aug. 17;1433(1-2):321-6; Ferranti P, et al., Differential splicing of pre-messenger RNA produces multiple forms of mature caprine alpha(s1)-casein, Eur J Biochem. 1997 Oct. 1;249(1):1-7. For PCR-based Validation: Wellmann S, et al., Specific reverse transcription-PCR quantification of vascular endothelial growth factor (VEGF) splice variants by LightCycler technology, Clin Chem. 2004 April 47(4):654-60; Jia, H. P., et al., Discovery of new human beta-defensins using a genomics-based approach, Gene. 2001 Jan. 24; 263(1-2):211-8. For PCR-based and 5′ RACE Validation: Brigle, K. E., et al., Organization of the murine reduced folate carrier gene and identification of variant splice forms, Biochem Biophys Acta. 1997 Aug. 7;1353(2): 191-8).

It is known in the art that genomic regions are modulated in cancers. When the genomic region to which 108P5H8 maps is modulated in a particular cancer, the variants of 108P5H8 are modulated as well. Disclosed herein is that 108P5H8 has a particular expression profile. Variants of 108P5H8 that are structurally and/or functionally similar to 108P5H8 share this expression pattern, thus serving as tumor-associated markers/antigens.

Example 3 Chromosomal Localization

Chromosomal localization can implicate genes in disease pathogenesis. Several chromosome mapping approaches are available, including fluorescent in situ hybridization (FISH), human/hamster Genebridge4 radiation hybrid (RH) panels (Walter et al., 1994; Nature Genetics 7:22; Research Genetics, Huntsville Ala.), human-rodent somatic cell hybrid panels such as is available from the Coriell Institute (Camden, N.J.), and genomic viewers utilizing BLAST homologies to sequenced and mapped genomic clones (NCBI, Bethesda, Md.).

The chromosomal localization of 108P5H8 using the GeneBridge4 radiation hybrid panel was performed using the the following PCR primers:

(SEQ. ID. No.: 2596) 108P5H8.1 5′ TGCACACTGGACTTCGTAGAGTAA 3′ (SEQ. ID. No.: 2597) 108P5H8.2 5′ AAAGCTGTGAGAGTGGCTGAGAAA 3′

The resulting mapping vector for the 93 radiation hybrid panel DNAs was: 10010100110100010100000000000011010000000120110000101100010000101110001010001000002011 0110121

This mapping vector and the mapping program placed 108P5H8 to chromosome 15q 15 .2-q21.1.

Example 4 Expression Analysis of 108P5H8 in Normal Tissues and Patient Specimens

Expression of 108P5H8 was analyzed by RT-PCR (FIG. 10). First strand cDNA was prepared from vital pool 1 (VP1: liver, lung and kidney), vital pool 2 (VP2, pancreas, colon and stomach), prostate xenograft pool (LAPC-4AD, LAPC-4AI, LAPC-9AD, LAPC-9AI), prostate cancer pool, bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, ovary cancer pool, breast cancer pool, metastasis cancer pool, pancreas cancer pool, and from prostate cancer metastasis to lymph node from two different patients. Normalization was performed by PCR using primers to actin and GAPDH. Semi-quantitative PCR, using primers to 108P5H8, was performed at 26 and 30 cycles of amplification. Strong expression of 108P5H8 was observed in prostate cancer xenograft pool, prostate cancer pool and in the 2 different prostate cancer metastasis samples. Lower expression was detected in bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, ovary cancer pool, breast cancer pool, metastasis pool, pancreas cancer pool, VP1 and VP2.

Extensive Northern blot analysis of 108P5H8 in 16 human normal tissues confirmed the expression observed by RT-PCR (FIG. 11). An approximately 7 kb 108P5H8 transcript was strongly expressed in prostate. Significantly lower expression was detected in other tissues.

FIG. 11C shows expression of 108P5H8 in prostate cancer xenografts. RNA was extracted from prostate cancer xenografts, LAPC-4AD, LAPC-4AI, LAPC-9AD, and LAPC-9AI. Northern blot with 10 μg of total RNA/lane was probed with 108P5H8 SSH sequence. Results showed expression of 108P5H8 in all four xenograft tissues. More detailed analysis of the xenografts shows that 108P5H8is highly expressed in the xenografts even when grown within the tibia of mice (FIG. 12). The expression is increased when the LAPC-4 xenograft is grown within a human bone implant (LAPC-4 AD²) It is possible that the human bone environment increases and/or induces the expression of 108P5H8. Northern blot analysis also showed that 108P5H8 is expressed in all human cancer cell lines tested such as prostate, bladder, brain, lung, kidney, breast, testis and ovary cancer cell lines (FIG. 13).

Expression of 108P5H8 was assayed in a panel of human cancers (T) and their respective matched normal tissues (N) on RNA dot blots (FIG. 14). 108P5H8 expression was detected in prostate, kidney, uterus and stomach cancers. The expression detected in some normal adjacent tissues (isolated from diseased tissues), but not in normal tissues (isolated from healthy donors), may indicate that these tissues are not fully normal and that 108P5H8 may be expressed in early stage tumors. 108P5H8 was also expressed in all 9 human cancer cell lines tested.

To test expression of 108P5H8 in patient cancer specimens, RNA was extracted from prostate cancer tumors (T) and their matched normal adjacent tissue (N_(AT)). Northern blots with 10 μg of total RNA/lane were probed with 108P5H8 SSH sequence (FIG. 15). Results showed expression of 108P5H8 in all prostate patient specimens tested.

108P5H8 was isolated from an experiment where cDNA derived from LNCaP cells that was androgen-deprived (by growing in the presence of charcoal-stripped serum) was subtracted from cDNA derived from LNCaP cells that were stimulated with mibolerone. To assess whether 108P5H8 is androgen-regulated, LNCaP cells were grown in charcoal-stripped medium and stimulated with the synthetic androgen mibolerone, for either 14 or 24 hours (FIG. 16). Northern blots with 10 μg of total RNA/lane were probed with either the 108P5H8 sequence (FIG. 16A). Results show expression of 108P5H8 is not regulated by androgen. The experimental samples were confirmed by testing for the expression of the androgen-regulated prostate cancer gene PSA (FIG. 16B). This experiment shows that, as expected, PSA levels go down in presence of charcoal-stripped serum, and expression is induced at 14 and 24 hours in presence of the synthetic androgen. A picture of the ethidium-bromide staining of the RNA gel is also presented (FIG. 16C).

FIG. 17 shows expression of 108P5H8 in cancer metastasis patient specimens. RNA was extracted from prostate cancer metastasis to lymph node isolated from 2 different patients, as well as from normal bladder (NB), normal kidney (NK), normal lung (NL), normal breast (NBr), normal ovary (NO), and normal pancreas (NPa). Northern blots with 10 μg of total RNA/lane was probed with 108P5H8 sequence. The results show expression of 108P5H8 in both cancer metastasis samples but not in normal tissues.

108P5H8 expression showed prostate restricted expression. Its strong expression detected in normal prostate and prostate cancer tissues and the low expression detected in other normal tissues indicate that 108P5H8 is therapeutic and prophylactic target and a diagnostic and prognostic marker for human cancers.

Example 5 Production of Recombinant 108P5H8 in Prokaryotic Systems

To express recombinant 108P5H8 in prokaryotic cells, the full or partial length 108P5H8 cDNA sequences can be cloned into any one of a variety of expression vectors known in the art. One or more of the following regions of 108P5H8 are expressed in these constructs, amino acids 1 to 429 of variant 1 or variant 2; or amino acids 1 to 388 of variant 4, or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acids from 108P5H8, variants, or analogs thereof. In certain embodiments a region of 108P5H8 is expressed that encodes an amino acid not shared amongst at least one of the variants, such as a construct encoding the D to E mutation at amino acid 30.

A. In Vitro Transcription and Translation Constructs:

pCRII: To generate 108P5H8 sense and anti-sense RNA probes for RNA in situ investigations, pCRII constructs (Invitrogen, Carlsbad Calif.) are generated encoding either all or fragments of a 108P5H8 cDNA. The pCRII vector has Sp6 and T7 promoters flanking the insert to drive the transcription of 108P5H8 RNA for use as probes in RNA in situ hybridization experiments. These probes are used to analyze the cell and tissue expression of 108P5H8 at the RNA level. Transcribed 108P5H8 RNA representing the cDNA amino acid coding region of the 108P5H8 gene is used in in vitro translation systems such as the TnT™ Coupled Reticulolysate System (Promega, Corp., Madison, Wis.) to synthesize 108P5H8 protein.

B. Bacterial Constructs:

pGEX Constructs: To generate recombinant 108P5H8 proteins in bacteria that are fused to the Glutathione S-transferase (GST) protein, all or parts of a 108P5H8 cDNA protein coding sequence are fused to the GST gene by cloning into pGEX-6P-1 or any other GST-fusion vector of the pGEX family (Amersham Pharmacia Biotech, Piscataway, N.J.). These constructs allow controlled expression of recombinant 108P5H8 protein sequences with GST fused at the amino-terminus and a six histidine epitope (6× His) at the carboxyl-terminus. The GST and 6× His tags permit purification of the recombinant fusion protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-GST and anti-His antibodies. The 6× His tag is generated by adding 6 histidine codons to the cloning primer at the 3′ end, e.g., of the open reading frame (ORF). A proteolytic cleavage site, such as the PreScission™ recognition site in pGEX-6P-1, may be employed such that it permits cleavage of the GST tag from 108P5H8-related protein. The ampicillin resistance gene and pBR322 origin permits selection and maintenance of the pGEX plasmids in E. coli.

In one embodiment, a GST-fusion protein was constructed and expressed that encoded amino acids 1-112. This protein was used as an immunogen for generation of a 108P5H8 specific polyclonal antibody as described in example 8.

pMAL Constructs: To generate, in bacteria, recombinant 108P5H8 proteins that are fused to maltose-binding protein (MBP), all or parts of a 108P5H8 cDNA protein coding sequence are fused to the MBP gene by cloning into the pMAL-c2× and pMAL-p2× vectors (New England Biolabs, Beverly, Mass.). These constructs allow controlled expression of recombinant 108P5H8 protein sequences with MBP fused at the amino-terminus and a 6× His epitope tag at the carboxyl-terminus. The MBP and 6× His tags permit purification of the recombinant protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-MBP and anti-His antibodies. The 6× His epitope tag is generated by adding 6 histidine codons to the 3′ cloning primer. A Factor Xa recognition site permits cleavage of the pMAL tag from 108P5H8. The pMAL-c2× and pMAL-p2× vectors are optimized to express the recombinant protein in the cytoplasm or periplasm respectively. Periplasm expression enhances folding of proteins with disulfide bonds.

pET Constructs: To express 108P5H8 in bacterial cells, all or parts of a 108P5H8 cDNA protein coding sequence are cloned into the pET family of vectors (Novagen, Madison, Wis.). These vectors allow tightly controlled expression of recombinant 108P5H8 protein in bacteria with and without fusion to proteins that enhance solubility, such as NusA and thioredoxin (Trx), and epitope tags, such as 6× His and S-Tag™ that aid purification and detection of the recombinant protein. For example, constructs are made utilizing pET NusA fusion system 43.1 such that regions of a 108P5H8 protein are expressed as amino-terminal fusions to NusA.

C. Yeast Constructs:

pESC Constructs: To express 108P5H8 in the yeast species Saccharomyces cerevisiae for generation of recombinant protein and functional studies, all or parts of a 108P5H8 cDNA protein coding sequence are cloned into the pESC family of vectors each of which contain 1 of 4 selectable markers, HIS3, TRP1, LEU2, and URA3 (Stratagene, La Jolla, Calif.). These vectors allow controlled expression from the same plasmid of up to 2 different genes or cloned sequences containing either Flag™ or Myc epitope tags in the same yeast cell. This system is useful to confirm protein-protein interactions of 108P5H8. In addition, expression in yeast yields similar post-translational modifications, such as glycosylations and phosphorylations, that are found when expressed in eukaryotic cells.

pESP Constructs: To express 108P5H8 in the yeast species Saccharomyces pombe, all or parts of a 108P5H8 cDNA protein coding sequence are cloned into the pESP family of vectors. These vectors allow controlled high level of expression of a 108P5H8 protein sequence that is fused at either the amino terminus or at the carboxyl terminus to GST which aids purification of the recombinant protein. A Flag™ epitope tag allows detection of the recombinant protein with anti-Flag™ antibody.

Example 6 Production of Recombinant 108P5H8 in Eukaryotic Systems

A. Mammalian Constructs:

To express recombinant 108P5H8 in eukaryotic cells, the full or partial length 108P5H8 cDNA sequences can be cloned into any one of a variety of expression vectors known in the art. One or more of the following regions of 108P5H8 are expressed in these constructs, amino acids 1 to 429 of variant, variant 2 or variant 3; or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acids from 108P5H8, variants, or analogs thereof. In certain embodiments a region of 108P5H8 is expressed that encodes an amino acid not shared amongst at least two variants.

The constructs can be transfected into any one of a wide variety of mammalian cells such as 293T cells. Transfected 293T cell lysates are probed with an anti-His epitope tag antibody or with anti-108P5H8 polyclonal antibodies to verify protein expression.

pcDNA4/HisMax Constructs: To express 108P5H8 in mammalian cells, a 108P5H8 ORF, or portions thereof, of 108P5H8 are cloned into pcDNA4/HisMax Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter and the SP16 translational enhancer. The recombinant protein has Xpress™ and six histidine (6× His) epitopes fused to the amino-terminus. The pcDNA4/HisMax vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Zeocin resistance gene allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli.

pcDNA3.1/MycHis Constructs: To express 108P5H8 in mammalian cells, a 108P5H8 ORF, or portions thereof, of 108P5H8 with a consensus Kozak translation initiation site were cloned into pcDNA3.1/MycHis Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant proteins have the myc epitope and 6× His epitope fused to the carboxyl-terminus. The pcDNA3.1/MycHis vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability, along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene can be used, as it allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli. The pcDNA3.1/MycHis construct encoding 108P5H8 was transfected into 293T cells. Expression of 108P5H8 was assayed by flow cytometry and using anti-His antibody as well as polyclonal anti-108P5H8 antibody (FIG. 22). Results show that 108P5H8 protein was expressed and was localized to the cell surface.

pcDNA3.1/CT-GFP-TOPO Construct: To express 108P5H8 in mammalian cells and to allow detection of the recombinant proteins using fluorescence, a 108P5H8 ORF, or portions thereof, with a consensus Kozak translation initiation site are cloned into pcDNA3.1/CT-GFP-TOPO (Invitrogen, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant proteins have the Green Fluorescent Protein (GFP) fused to the carboxyl-terminus facilitating non-invasive, in vivo detection and cell biology studies. The pcDNA3.1CT-GFP-TOPO vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli. Additional constructs with an amino-terminal GFP fusion are made in pcDNA3.1/NT-GFP-TOPO spanning the entire length of a 108P5H8 protein.

PAPtag: A 108P5H8 ORF, or portions thereof, is cloned into pAPtag-5 (GenHunter Corp. Nashville, Tenn.). This construct generates an alkaline phosphatase fusion at the carboxyl-terminus of a 108P5H8 protein while fusing the IgGκ signal sequence to the amino-terminus. Constructs are also generated in which alkaline phosphatase with an amino-terminal IgGκ signal sequence is fused to the amino-terminus of a 108P5H8 protein. The resulting recombinant 108P5H8 proteins are optimized for secretion into the media of transfected mammalian cells and can be used to identify proteins such as ligands or receptors that interact with 108P5H8 proteins. Protein expression is driven from the CMV promoter and the recombinant proteins also contain myc and 6× His epitopes fused at the carboxyl-terminus that facilitates detection and purification. The Zeocin resistance gene present, in the vector allows for selection of mammalian cells expressing the recombinant protein and the ampicillin resistance gene permits selection of the plasmid in E. coli.

ptag5: A 108P5H8 ORF, or portions thereof, is cloned into pTag-5. This vector is similar to pAPtag but without the alkaline phosphatase fusion. This construct generates 108P5H8 protein with an amino-terminal IgGκ signal sequence and myc and 6× His epitope tags at the carboxyl-terminus that facilitate detection and affinity purification. The resulting recombinant 108P5H8 protein is optimized for secretion into the media of transfected mammalian cells, and is used as immunogen or ligand to identify proteins such as ligands or receptors that interact with the 108P5H8 proteins. Protein expression is driven from the CMV promoter. The Zeocin resistance gene present in the vector allows for selection of mammalian cells expressing the protein, and the ampicillin resistance gene permits selection of the plasmid in E. coli.

PsecFc: A 108P5H8 ORF, or portions thereof, is also cloned into psecFc. The psecFc vector was assembled by cloning the human immunoglobulin G1 (IgG) Fc (hinge, CH2, CH3 regions) into pSecTag2 (Invitrogen, Calif.). This construct generates an IgG1 Fc fusion at the carboxyl-terminus of the 108P5H8 proteins, while fusing the IgGK signal sequence to N-terminus. 108P5H8 fusions utilizing the murine IgG1 Fc region are also used. The resulting recombinant 108P5H8 proteins are optimized for secretion into the media of transfected mammalian cells, and can be used as immunogens or to identify proteins such as ligands or receptors that interact with 108P5H8 protein. Protein expression is driven from the CMV promoter. The hygromycin resistance gene present in the vector allows for selection of mammalian cells that express the recombinant protein, and the ampicillin resistance gene permits selection of the plasmid in E. coli.

pSRα Constructs: To generate mammalian cell lines that express 108P5H8 constitutively, 108P5H8 ORF, or portions thereof, of 108P5H8 were cloned into pSRα constructs. Amphotropic and ecotropic retroviruses are generated by transfection of pSRα constructs into the 293T-10A1 packaging line or co-transfection of pSRα and a helper plasmid (containing deleted packaging sequences) into the 293 cells, respectively. The retrovirus is used to infect a variety of mammalian cell lines, resulting in the integration of the cloned gene, 108P5H8, into the host cell-lines. Protein expression is driven from a long terminal repeat (LTR). The Neomycin resistance gene present in the vector allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permit selection and maintenance of the plasmid in E. coli. The retroviral vectors can thereafter be used for infection and generation of various cell lines using, for example, PC3, NIH 3T3, TsuPr1, 293 or rat-1 cells. Results of expression of 108P5H8 protein driven from the pSRα in PC3 and NIH3T3 cells are shown in FIG. 24.

Additional pSRα constructs are made that fuse an epitope tag such as the FLAG™ tag to the carboxyl-terminus of 108P5H8 sequences to allow detection using anti-Flag antibodies. For example, the FLAG™ sequence 5′ gat tac aag gat gac gac gat aag 3′ (SEQ. ID. No.: 2598) is added to cloning primer at the 3′ end of the ORF. Additional pSRα constructs are made to produce both amino-terminal and carboxyl-terminal GFP and myc/6× His fusion proteins of the full-length 108P5H8 proteins.

Additional Viral Vectors: Additional constructs are made for viral-mediated delivery and expression of 108P5H8. High virus titer leading to high level expression of 108P5H8 is achieved in viral delivery systems such as adenoviral vectors and herpes amplicon vectors. A 108P5H8 coding sequences or fragments thereof are amplified by PCR and subcloned into the AdEasy shuttle vector (Stratagene). Recombination and virus packaging are performed according to the manufacturer's instructions to generate adenoviral vectors. Alternatively, 108P5H8 coding sequences or fragments thereof are cloned into the HSV-1 vector (Imgenex) to generate herpes viral vectors. The viral vectors are thereafter used for infection of various cell lines such as PC3, NIH 3T3, 293 or rat-1 cells.

Regulated Expression Systems: To control expression of 108P5H8 in mammalian cells, coding sequences of 108P5H8, or portions thereof, are cloned into regulated mammalian expression systems such as the T-Rex System (Invitrogen), the GeneSwitch System (Invitrogen) and the tightly-regulated Ecdysone System (Sratagene). These systems allow the study of the temporal and concentration dependent effects of recombinant 108P5H8. These vectors are thereafter used to control expression of 108P5H8 in various cell lines such as PC3, NIH 3T3, 293 or rat-1 cells.

B. Baculovirus Expression Systems

To generate recombinant 108P5H8 proteins in a baculovirus expression system, 108P5H8 ORF, or portions thereof, are cloned into the baculovirus transfer vector pBlueBac 4.5 (Invitrogen), which provides a His-tag at the N-terminus. Specifically, pBlueBac-108P5H8 is co-transfected with helper plasmid pBac-N-Blue (Invitrogen) into SF9 (Spodoptera frugiperda) insect cells to generate recombinant baculovirus (see Invitrogen instruction manual for details). Baculovirus is then collected from cell supernatant and purified by plaque assay.

Recombinant 108P5H8 protein is then generated by infection of HighFive insect cells (Invitrogen) with purified baculovirus. Recombinant 108P5H8 protein can be detected using anti-108P5H8 or anti-His-tag antibody. 108P5H8 protein can be purified and used in various cell-based assays or as immunogen to generate polyclonal and monoclonal antibodies specific for 108P5H8.

Example 7 Antigenicity Profiles and Secondary Structure

FIG. 5, FIG. 6, FIG. 7, FIG. 8, and FIG. 9 depict graphically five amino acid profiles of the 108P5H8 amino acid sequence (variant 1), each assessment is available by accessing the ProtScale website on the ExPasy molecular biology server.

These profiles: FIG. 5, Hydrophilicity, (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828); FIG. 6, Hydropathicity, (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105-132); FIG. 7, Percentage Accessible Residues (Janin J., 1979 Nature 277:491-492); FIG. 8, Average Flexibility, (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242-255); FIG. 9, Beta-turn (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294); and optionally others available in the art, such as on the ProtScale website, were used to identify antigenic regions of 108P5H8 protein. Each of the above amino acid profiles of 108P5H8 were generated using the following ProtScale parameters for analysis: 1) A window size of 9; 2) 100% weight of the window edges compared to the window center; and, 3) amino acid profile values normalized to lie between 0 and 1.

Hydrophilicity (FIG. 5), Hydropathicity (FIG. 6) and Percentage Accessible Residues (FIG. 7) profiles were used to determine stretches of hydrophilic amino acids (i.e., values greater than 0.5 on the Hydrophilicity and Percentage Accessible Residues profiles, and values less than 0.5 on the Hydropathicity profile). Such regions are likely to be exposed to the aqueous environment, be present on the surface of the protein, and thus available for immune recognition, such as by antibodies.

Average Flexibility (FIG. 8) and Beta-turn (FIG. 9) profiles determine stretches of amino acids (i.e., values greater than 0.5 on the Beta-turn profile and the Average Flexibility profile) that are not constrained in secondary structures such as beta sheets and alpha helices. Such regions are also more likely to be exposed on the protein and thus accessible to immune recognition, such as by antibodies.

Antigenic sequences of the full length 108P5H8 protein (variant 1) indicated, e.g., by the profiles set forth in FIG. 5, FIG. 6, FIG. 7, FIG. 8, and/or FIG. 9 are used to prepare immunogens, either peptides or nucleic acids that encode them, to generate therapeutic and diagnostic anti-108P5H8 antibodies. The immunogen can be any 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more than 50 contiguous amino acids, or the corresponding nucleic acids that encode them, from 108P5H8 protein. In particular, peptide immunogens of the invention can comprise, a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 429 that includes an amino acid position having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5; a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 429 that includes an amino acid position having a value less than 0.5 in the Hydropathicity profile of FIG. 6; a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 429 that includes an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7; a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 429 that includes an amino acid position having a value greater than 0.5 in the Average Flexibility profile on FIG. 8; and, a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 429 that includes an amino acid position having a value greater than 0.5 in the Beta-turn profile of FIG. 9. Peptide immunogens of the invention can also comprise nucleic acids that encode any of the forgoing.

All immunogens of the invention, peptide or nucleic acid, can be embodied in human unit dose form, or comprised by a composition that includes a pharmaceutical excipient compatible with human physiology.

The secondary structure of 108P5H8, namely the predicted presence and location of alpha helices, extended strands, and random coils, is predicted from the primary amino acid sequence of 108P5H8 variant 1 using the HNN—Hierarchical Neural Network method (Guermeur, 1997 ), accessed from the ExPasy molecular biology server. The analysis indicates that 108P5H8 is composed of 49.88% alpha helix, 11.66% extended strand, and 38.46% random coil (FIG. 18).

Analysis for the potential presence of transmembrane domains in 108P5H8 was carried out using a variety of transmembrane prediction algorithms accessed from the ExPasy molecular biology server. The programs predict the presence of 6 transmembrane domains in 108P5H8. Shown graphically in FIGS. 19A and 19B are the results of analysis using the TMpred and TMHMM prediction programs, respectively, depicting the location of the 6 transmembrane domains. The results of each program, namely the amino acids encoding the transmembrane domains are summarized in Table XXI.

Example 8 Generation of 108P5H8 Polyclonal Antibodies

Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. In addition to immunizing with the full length 108P5H8 protein, computer algorithms are employed in design of immunogens that, based on amino acid sequence analysis contain characteristics of being antigenic and available for recognition by the immune system of the immunized host (see the Example entitled “Antigenicity Profiles and Secondary Structure”). Such regions would be predicted to be hydrophilic, flexible, in beta-turn conformations, and be exposed on the surface of the protein (see, e.g., FIG. 5, FIG. 6, FIG. 7, FIG. 8, or FIG. 9 for amino acid profiles that indicate such regions of 108P5H8).

For example, 108P5H8 recombinant bacterial fusion proteins or peptides containing hydrophilic, flexible, beta-turn regions of 108P5H8 are used as antigens to generate polyclonal antibodies in New Zealand White rabbits. Such regions often reside in extracellular and intracellular loops between transmembrane domains. For example, such regions include, but are not limited to, amino acids 1-112 (intracellular amino terminus), amino acids 139-152 (1^(st) extracellular loop), amino acids 201-214 (second extracellular loop), amino acids 294-307 (third extracellular loop), or amino acids 336-429 (carboxyl terminus). It is useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include, but are not limited to, keyhole limpet hemocyanin (KLH), serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. In one embodiment, a peptide encoding amino acids 294-307 of 108P5H8 is conjugated to KLH and used to immunize the rabbit. Alternatively the immunizing agent may include all or portions of a 108P5H8 protein, analogs or fusion proteins thereof. For example, a 108P5H8 amino acid sequence can be fused using recombinant DNA techniques to any one of a variety of fusion protein partners that are well known in the art, such as glutathione-S-transferase (GST) and HIS tagged fusion proteins. Such fusion proteins are purified from induced bacteria using the appropriate affinity matrix.

In one embodiment, a GST-fusion protein encoding amino acids 1-112 of 108P5H8 was produced and purified and used to immunize a rabbit. This polyclonal antibody specifically recognized both recombinant and endogenous 108P5H8 protein in cells and tissues. FIG. 20 shows non-androgen-regulated expression of 108P5H8 in the prostate cancer cell lines LNCaP and LAPC4. The expression of 108P5H8 is cell surface as detected by the polyclonal antibody in LNCaP and LAPC4 cells (FIG. 21) and when overexpressed in 293T cells (FIG. 22). FIG. 23 shows expression in prostate patient cancer samples, including metastatic disease, indicating the protein is a therapeutic target in both androgen-dependent and independent prostate cancer. 108P5H8 is also expressed in ovarian cancer, but not in normal ovary (FIG. 23), indicating the protein is a therapeutic and diagnostic target in this disease as well.

In addition to GST-fusions, other recombinant bacterial fusion proteins that can be employed include maltose binding protein, LacZ, thioredoxin, NusA, or an immunoglobulin constant region (see the section entitled “Production of 108P5H8 in Prokaryotic Systems” and Current Protocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubul et al. eds., 1995; Linsley, P. S., Brady, W., Urnes, M., Grosmaire, L., Damle, N., and Ledbetter, L. (1991) J. Exp. Med. 174, 561-566).

In addition to bacterial-derived fusion proteins, mammalian-expressed protein antigens are also used. These antigens are expressed from mammalian expression vectors such as the Tag5 and Fc-fusion vectors (see the section entitled “Production of Recombinant 108P5H8 in Eukaryotic Systems”), and retain post-translational modifications such as glycosylations found in native protein. In one embodiment, the first extracellular loop of 108P5H8 (amino acids 139-152) is cloned into the Tag5 mammalian secretion-vector. The recombinant protein is purified by metal chelate chromatography from tissue culture supernatants of 293T cells stably expressing the recombinant vector. The purified Tag5 108P5H8 protein is then used as immunogen.

During the immunization protocol, it is useful to mix or emulsify the antigen in adjuvants that enhance the immune response of the host animal. Examples of adjuvants include, but are not limited to, complete Freund's adjuvant (CFA) and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).

In a typical protocol, rabbits are initially immunized subcutaneously with up to 200 μg, typically 100-200 μg, of fusion protein or peptide conjugated to KLH mixed in complete Freund's adjuvant (CFA). Rabbits are then injected subcutaneously every two weeks with up to 200 μg, typically 100-200 μg, of the immunogen in incomplete Freund's adjuvant (IFA). Test bleeds are taken approximately 7-10 days following each immunization and used to monitor the titer of the antiserum by ELISA.

To test reactivity and specificity of immune serum, such as the rabbit serum derived from immunization with Tag5 108P5H8 protein or KLH-coupled peptide encoding amino acids 294-307, the full-length 108P5H8 cDNA is cloned into pcDNA 3.1 myc-his expression vector (Invitrogen, see the Example entitled “Production of Recombinant 108P5H8 in Eukaryotic Systems”). After transfection of the constructs into 293T cells, cell lysates are probed with the anti-108P5H8 serum and with anti-His antibody (Santa Cruz Biotechnologies, Santa Cruz, Calif.) to determine specific reactivity to denatured 108P5H8 protein using the Western blot technique (FIG. 20). Immunoprecipitation and flow cytometric analyses of 293T and other recombinant 108P5H8-expressing cells determine recognition of native protein by the antiserum (FIG. 22, FIG. 24). In addition, Western blot, immunoprecipitation, fluorescent microscopy, and flow cytometric techniques using cells that endogenously express 108P5H8 are carried out to test specificity (FIG. 20, FIG. 21).

The anti-serum from the Tag5 108P5H8 immunized rabbit is affinity purified by passage over a column composed of the Tag5 antigen covalently coupled to Affigel matrix (BioRad, Hercules, Calif.). The serum is then further purified by protein G affinity chromatography to isolate the IgG fraction. Serum from rabbits immunized with the GST-fusion protein was purified by depletion of antibodies reactive to the fusion partner sequence (GST) by passage over an affinity column containing the GST alone and then by passage back over a GST-108P5H8 column to isolate gene specific antibodies. Sera from other His-tagged antigens and peptide immunized rabbits as well as fusion partner depleted sera are affinity purified by passage over a column matrix composed of the original protein immunogen or free peptide.

Example 9 Generation of 108P5H8 Monoclonal Antibodies (mAbs)

In one embodiment, therapeutic mAbs to 108P5H8 comprise those that react with epitopes of the protein that would disrupt or modulate the biological function of 108P5H8, for example those that would disrupt its interaction with ligands, proteins, or substrates that mediate its biological activity. Immunogens for generation of such mAbs include those designed to encode or contain an entire 108P5H8 protein or its variants or regions of 108P5H8 protein predicted to be exposed on the cell surface and/or antigenic from computer analysis of the amino acid sequence (see, e.g., FIG. 5, FIG. 6, FIG. 7, FIG. 8, or FIG. 9, and the Example entitled “Antigenicity Profiles and Secondary Structure”). Immunogens include peptides, recombinant bacterial proteins, and mammalian expressed Tag 5 proteins and human and murine IgG FC fusion proteins. In addition, cells expressing high levels of 108P5H8, such as 293T-108P5H8 or 300.19-108P5H8 murine Pre-B cells, are used to immunize mice.

To generate mAbs to 108P5H8, mice are first immunized intraperitoneally (IP) with, typically, 10-50 μg of protein immunogen or 10⁷ 108P5H8-expressing cells mixed in complete Freund's adjuvant. Mice are then subsequently immunized IP every 2-4 weeks with, typically, 10-50 μg of protein immunogen or 10⁷ cells mixed in incomplete Freund's adjuvant. Alternatively, MPL-TDM adjuvant is used in immunizations. In addition to the above protein and cell-based immunization strategies, a DNA-based immunization protocol is employed in which a mammalian expression vector encoding 108P5H8 sequence is used to immunize mice by direct injection of the plasmid DNA. For example, the predicted third extracellular loop, amino acids 294-307 of 108P5H8, is cloned into the Tag5 mammalian secretion vector and the recombinant vector is used as immunogen. In another example the amino acids are cloned into an Fc-fusion secretion vector in which a 108P5H8 sequence is fused at the amino-terminus to an IgK leader sequence and at the carboxyl-terminus to the coding sequence of the human or murine IgG Fc region. This recombinant vector is then used as immunogen. The plasmid immunization protocols are used in combination with purified proteins expressed from the same vector and with cells expressing 108P5H8.

During the immunization protocol, test bleeds are taken 7-10 days following an injection to monitor titer and specificity of the immune response. Once appropriate reactivity and specificity is obtained as determined by ELISA, Western blotting, immunoprecipitation, fluorescence microscopy, and flow cytometric analyses, fusion and hybridoma generation is then carried out with established procedures well known in the art (see, e.g., Harlow and Lane, 1988).

In one embodiment, monoclonal antibodies are derived from immunization of mice with 300.19 cells engineered to express high levels of 108P5H8 (>30,000 molecules per cell). Balb C mice are initially immunized intraperitoneally with 10⁷ cells mixed in complete Freund's adjuvant. Mice are subsequently immunized every two weeks with 10⁷ cells mixed in incomplete Freund's adjuvant for a total of three immunizations. Reactivity and specificity of serum to the full length 108P5H8 protein is monitored by Western blotting, immunoprecipitation and flow cytometry using various cells engineered to overexpress 108P5H8 protein (FIG. 24). Mice showing the strongest reactivity are rested and given a final injection of cells in PBS and then sacrificed four days later. The spleens of the sacrificed mice are harvested and fused to SPO/2 myeloma cells using standard procedures (see, e.g., Harlow and Lane, 1988). Supernatants from HAT selected growth wells are, screened by ELISA, Western blot, immunoprecipitation, fluorescent microscopy, and flow cytometry to identify 108P5H8 specific antibody-producing clones.

The binding affinity of a 108P5H8 monoclonal antibody is determined using standard technologies. Affinity measurements quantify the strength of antibody to epitope binding and are used to help define which 108P5H8 monoclonal antibodies preferred, e.g., for diagnostic or therapeutic use, as appreciated by one of skill in the art. The BIAcore system (Uppsala, Sweden) is a preferred method for determining binding affinity. The BIAcore system uses surface plasmon resonance (SPR, Welford K. 1991, Opt. Quant. Elect. 23:1; Morton and Myszka, 1998, Methods in Enzymology 295: 268) to monitor biomolecular interactions in real time. BIAcore analysis conveniently generates association rate constants, dissociation rate constants, equilibrium dissociation constants, and affinity constants.

Example 10 HLA Class I and Class II Binding Assays

HLA class I and class II binding assays using purified HLA molecules are performed in accordance with disclosed protocols (e.g., PCT publications WO 94/20127 and WO 94/03205; Sidney et al., Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813 (1994)). Briefly, purified MHC molecules (5 to 500 nM) are incubated with various unlabeled peptide inhibitors and 1-10 nM ¹²⁵I-radiolabeled probe peptides as described. Following incubation, MHC-peptide complexes are separated from free peptide by gel filtration and the fraction of peptide bound is determined. Typically, in preliminary experiments, each MHC preparation is titered in the presence of fixed amounts of radiolabeled peptides to determine the concentration of HLA molecules necessary to bind 10-20% of the total radioactivity. All subsequent inhibition and direct binding assays are performed using these HLA concentrations.

Since under these conditions [label]<[HLA] and IC₅₀≧[HLA], the measured IC₅₀ values are reasonable approximations of the true K_(D) values. Peptide inhibitors are typically tested at concentrations ranging from 120 μg/ml to 1.2 ng/ml, and are tested in two to four completely independent experiments. To allow comparison of the data obtained in different experiments, a relative binding figure is calculated for each peptide by dividing the IC₅₀ of a positive control for inhibition by the IC₅₀ for each tested peptide (typically unlabeled versions of the radiolabeled probe peptide). For database purposes, and inter-experiment comparisons, relative binding values are compiled. These values can subsequently be converted back into IC50 nM values by dividing the IC₅₀ nM of the positive controls for inhibition by the relative binding of the peptide of interest. This method of data compilation is accurate and consistent for comparing peptides that have been tested on different days, or with different lots of purified MHC.

Binding assays as outlined above may be used to analyze HLA supermotif and/or HLA motif-bearing peptides.

Example 11 Identification of HLA Supermotif- and Motif-Bearing CTL Candidate Epitopes

HLA vaccine compositions of the invention can include multiple epitopes. The multiple epitopes can comprise multiple HLA supermotifs or motifs to achieve broad population coverage. This example illustrates the identification and confirmation of supermotif- and motif-bearing epitopes for the inclusion in such a vaccine composition. Calculation of population coverage is performed using the strategy described below.

Computer Searches and Algorithms for Identification of Supermotif and/or Motif-Bearing Epitopes

The searches performed to identify the motif-bearing peptide sequences in the Example entitled “Antigenicity Profiles” and Tables V-XVIII, XXII, and XXIII employ the protein sequence data from the gene product of 108P5H8 set forth in FIGS. 2 and 3.

Computer searches for epitopes bearing HLA Class I or Class II supermotifs or motifs are performed as follows. All translated 108P5H8 protein sequences are analyzed using a text string search software program to identify potential peptide sequences containing appropriate HLA binding motifs; such programs are readily produced in accordance with information in the art in view of known motif/supermotif disclosures. Furthermore, such calculations can be made mentally.

Identified A2-, A3-, and DR-supermotif sequences are scored using polynomial algorithms to predict their capacity to bind to specific HLA-Class I or Class II molecules. These polynomial algorithms account for the impact of different amino acids at different positions, and are essentially based on the premise that the overall affinity (or ΔG) of peptide-HLA molecule interactions can be approximated as a linear polynomial function of the type: “ΔG”=a _(1i) ×a _(2i) ×a _(3i) . . . ×a _(ni) where a_(ji) is a coefficient which represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. The crucial assumption of this method is that the effects at each position are essentially independent of each other (i.e., independent binding of individual side-chains). When residue j occurs at position i in the peptide, it is assumed to contribute a constant amount j_(i) to the free energy of binding of the peptide irrespective of the sequence of the rest of the peptide.

The method of derivation of specific algorithm coefficients has been described in Gulukota et al., J. Mol. Biol 267:1258-126, 1997; (see also Sidney et al., Human Immunol. 45:79-93, 1996; and Southwood et al., J. Immunol. 160:3363-3373, 1998). Briefly, for all i positions, anchor and non-anchor alike, the geometric mean of the average relative binding (ARB) of all peptides carrying j is calculated relative to the remainder of the group, and used as the estimate of j_(i). For Class II peptides, if multiple alignments are possible, only the highest scoring alignment is utilized, following an iterative procedure. To calculate an algorithm score of a given peptide in a test set, the ARB values corresponding to the sequence of the peptide are multiplied. If this product exceeds a chosen threshold, the peptide is predicted to bind. Appropriate thresholds are chosen as a function of the degree of stringency of prediction desired.

Selection of HLA-A2 Supertype Cross-Reactive Peptides

Protein sequences from 108P5H8 are scanned utilizing motif identification software, to identify 8-, 9- 10- and 11 -mer sequences containing the HLA-A2-supermotif main anchor specificity. Typically, these sequences are then scored using the protocol described above and the peptides corresponding to the positive-scoring sequences are synthesized and tested for their capacity to bind purified HLA-A*0201 molecules in vitro (HLA-A*0201 is considered a prototype A2 supertype molecule).

These peptides are then tested for the capacity to bind to additional A2-supertype molecules (A*0202, A*0203, A*0206, and A*6802). Peptides that bind to at least three of the five A2-supertype alleles tested are typically deemed A2-supertype cross-reactive binders. Preferred peptides bind at an affinity equal to or less than 500 nM to three or more HLA-A2 supertype molecules.

Selection of HLA-A3 Supermotif-Bearing Epitopes

The 108P5H8 protein sequence(s) scanned above is also examined for the presence of peptides with the HLA-A3-supermotif primary anchors. Peptides corresponding to the HLA A3 supermotif-bearing sequences are then synthesized and tested for binding to HLA-A*0301 and HLA-A*1101 molecules, the molecules encoded by the two most prevalent A3-supertype alleles. The peptides that bind at least one of the two alleles with binding affinities of ≦500 nM, often ≦200 nM, are then tested for binding cross-reactivity to the other common A3-supertype alleles (e.g., A*3101, A*3301, and A*6801) to identify those that can bind at least three of the five HLA-A3-supertype molecules tested.

Selection of HLA-B7 Supermotif Bearing Epitopes

The 108P5H8 protein(s) scanned above is also analyzed for the presence of 8-, 9- 10-, or 11-mer peptides with the HLA-B7-supermotif. Corresponding peptides are synthesized and tested for binding to HLA-B*0702, the molecule encoded by the most common B7-supertype allele (i.e., the prototype B7 supertype allele). Peptides binding B*0702 with IC₅₀ of ≦500 nM are identified using standard methods. These peptides are then tested for binding to other common B7-supertype molecules (e.g., B*3501, B*5101, B*5301, and B*5401). Peptides capable of binding to three or more of the five B7-supertype alleles tested are thereby identified.

Selection of A1 and A24 Motif-Baring Epitopes

To further increase population coverage, HLA-A1 and -A24 epitopes can also be incorporated into vaccine compositions. An analysis of the 108P5H8 protein can also be performed to identify HLA-A1- and A24-motif-containing sequences.

High affinity and/or cross-reactive binding epitopes that bear other motif and/or supermotifs are identified using analogous methodology.

Example 12 Confirmation of Immunogenicity

Cross-reactive candidate CTL A2-supermotif-bearing peptides that are identified as described herein are selected to confirm in vitro immunogenicity. Confirmation is performed using the following methodology:

Target Cell Lines for Cellular Screening:

The 0.221 A2.1 cell line, produced by transferring the HLA-A2.1 gene into the HLA-A, -B, -C null mutant human B-lymphoblastoid cell line 721.221, is used as the peptide-loaded target to measure activity of HLA-A2.1-restricted CTL. This cell line is grown in RPMI-1640 medium supplemented with antibiotics, sodium pyruvate, nonessential amino acids and 10% (v/v) heat inactivated FCS. Cells that express an antigen of interest, or transfectants comprising the gene encoding the antigen of interest, can be used as target cells to confirm the ability of peptide-specific CTLs to recognize endogenous antigen.

Primary CTL Induction Cultures:

Generation of Dendritic Cells (DC): PBMCs are thawed in RPMI with 30 μg/ml DNAse, washed twice and resuspended in complete medium (RPMI-1640 plus 5% AB human serum, non-essential amino acids, sodium pyruvate, L-glutamine and penicillin/streptomycin). The monocytes are purified by plating 10×10⁶ PBMC/well in a 6-well plate. After 2 hours at 37° C., the non-adherent cells are removed by gently shaking the plates and aspirating the supernatants. The wells are washed a total of three times with 3 ml RPMI to remove most of the non-adherent and loosely adherent cells. Three ml of complete medium containing 50 ng/ml of GM-CSF and 1,000 U/ml of IL-4 are then added to each well. TNFα is added to the DCs on day 6 at 75 ng/ml and the cells are used for CTL induction cultures on day 7.

Induction of CTL with DC and Peptide: CD8+ T-cells are isolated by positive selection with Dyna1 immunomagnetic beads (Dynabeads® M-450) and the detacha-bead® reagent. Typically about 200-250×10⁶ PBMC are processed to obtain 24×10⁶ CD8⁺ T-cells (enough for a 48-well plate culture). Briefly, the PBMCs are thawed in RPMI with 30 μg/ml DNAse, washed once with PBS containing 1% human AB serum and resuspended in PBS/1% AB serum at a concentration of 20×10⁶ cells/ml. The magnetic beads are washed 3 times with PBS/AB serum, added to the cells (140 μl beads/20×10⁶ cells) and incubated for 1 hour at 4° C. with continuous mixing. The beads and cells are washed 4× with PBS/AB serum to remove the nonadherent cells and resuspended at 100×10⁶ cells/ml (based on the original cell number) in PBS/AB serum containing 100 μl/ml detacha-bead® reagent and 30 μg/ml DNAse. The mixture is incubated for 1 hour at room temperature with continuous mixing. The beads are washed again with PBS/AB/DNAse to collect the CD8+ T-cells. The DC are collected and centrifuged at 1300 rpm for 5-7 minutes, washed once with PBS with 1% BSA, counted and pulsed with 40 μg/ml of peptide at a cell concentration of 1-2×10⁶/ml in the presence of 3 μg/ml β₂-microglobulin for 4 hours at 20° C. The DC are then irradiated (4,200 rads), washed 1 time with medium and counted again.

Setting up induction cultures: 0.25 ml cytokine-generated DC (at 1×10⁵ cells/ml) are co-cultured with 0.25 ml of CD8+ T-cells (at 2×10⁶ cell/ml) in each well of a 48-well plate in the presence of 10 ng/ml of IL-7. Recombinant human IL-1 is added the next day at a final concentration of 10 ng/ml and rhuman IL-2 is added 48 hours later at 10 IU/ml.

Restimulation of the induction cultures with peptide-pulsed adherent cells: Seven and fourteen days after the primary induction, the cells are restimulated with peptide-pulsed adherent cells. The PBMCs are thawed and washed twice with RPMI and DNAse. The cells are resuspended at 5×10⁶ cells/ml and irradiated at ˜4200 rads. The PBMCs are plated at 2×10⁶ in 0.5 ml complete medium per well and incubated for 2 hours at 37° C. The plates are washed twice with RPMI by tapping the plate gently to remove the nonadherent cells and the adherent cells pulsed with 10 μg/ml of peptide in the presence of 3 μg/ml β₂ microglobulin in 0.25 ml RPMI/5% AB per well for 2 hours at 37° C. Peptide solution from each well is aspirated and the wells are washed once with RPMI. Most of the media is aspirated from the induction cultures (CD8+ cells) and brought to 0.5 ml with fresh media. The cells are then transferred to the wells containing the peptide-pulsed adherent cells. Twenty four hours later recombinant human IL-10 is added at a final concentration of 10 ng/ml and recombinant human IL2 is added the next day and again 2-3 days later at 50 IU/ml (Tsai et al., Critical Reviews in Immunology 18(1-2):65-75, 1998). Seven days later, the cultures are assayed for CTL activity in a ⁵¹Cr release assay. In some experiments the cultures are assayed for peptide-specific recognition in the in situ IFNγ ELISA at the time of the second restimulation followed by assay of endogenous recognition 7 days later. After expansion, activity is measured in both assays for a side-by-side comparison.

Measurement of CTL Lytic Activity by ⁵¹Cr Release.

Seven days after the second restimulation, cytotoxicity is determined in a standard (5 hr) ⁵¹Cr release assay by assaying individual wells at a single E:T. Peptide-pulsed targets are prepared by incubating the cells with 10 μg/ml peptide overnight at 37° C.

Adherent target cells are removed from culture flasks with trypsin-EDTA. Target cells are labeled with 200 μCi of ⁵¹Cr sodium chromate (Dupont, Wilmington, Del.) for 1 hour at 37° C. Labeled target cells are resuspended at 10⁶ per ml and diluted 1:10 with K562 cells at a-concentration of 3.3×10⁶/ml (an NK-sensitive erythroblastoma cell line used to reduce non-specific lysis). Target cells (100 μl) and effectors (100 μl) are plated in 96 well round-bottom plates and incubated for 5 hours at 37° C. At that time, 100 μl of supernatant are collected from each well and percent lysis is determined according to the formula: [(cpm of the test sample−cpm of the spontaneous ⁵¹Cr release sample)/(cpm of the maximal ⁵¹Cr release sample−cpm of the spontaneous ⁵¹Cr release sample)]×100.

Maximum and spontaneous release are determined by incubating the labeled targets with 1% Triton X-100 and media alone, respectively. A positive culture is defined as one in which the specific lysis (sample-background) is 10% or higher in the case of individual wells and is 15% or more at the two highest E:T ratios when expanded cultures are assayed.

In situ Measurement of Human IFNγ Production as an Indicator of Peptide-Specific and Endogenous Recognition

Immulon 2 plates are coated with mouse anti-human IFNγ monoclonal antibody (4 μg/ml 0.1M NaHCO₃, pH8.2) overnight at 4° C. The plates are washed with Ca²⁺, Mg²⁺-free PBS/0.05% Tween 20 and blocked with PBS/10% FCS for two hours, after which the CTLs (100 μl/well) and targets (100 μl/well) are added to each well, leaving empty wells for the standards and blanks (which received media only). The target cells, either peptide-pulsed or endogenous targets, are used at a concentration of 1×10⁶ cells/ml. The plates are incubated for 48 hours at 37° C. with 5% CO₂.

Recombinant human IFN-gamma is added to the standard wells starting at 400 pg or 1200 pg/100 microliter/well and the plate incubated for two hours at 37° C. The plates are washed and 100 μl of biotinylated mouse anti-human IFN-gamma monoclonal antibody (2 microgram/ml in PBS/3% FCS/0.05% Tween 20) are added and incubated for 2 hours at room temperature. After washing again, 100 microliter HRP-streptavidin (1:4000) are added and the plates incubated for one hour at room temperature. The plates are then washed 6× with wash buffer, 100 microliter/well developing solution (TMB 1:1) are added, and the plates allowed to develop for 5-15 minutes. The reaction is stopped with 50 microliter/well 1M H₃PO₄ and read at OD450. A culture is considered positive if it measured at least 50 pg of IFN-gamma/well above background and is twice the background level of expression.

CTL Expansion.

Those cultures that demonstrate specific lytic activity against peptide-pulsed targets and/or tumor targets are expanded over a two week period with anti-CD3. Briefly, 5×10⁴ CD8+ cells are added to a T25 flask containing the following: 1×10⁶ irradiated (4,200 rad) PBMC (autologous or allogeneic) per ml, 2×10⁵ irradiated (8,000 rad) EBV-transformed cells per ml, and OKT3 (anti-CD3) at 30 ng per ml in RPMI-1640 containing 10% (v/v) human AB serum, non-essential amino acids, sodium pyruvate, 25 μM 2-mercaptoethanol, L-glutamine and penicillin/streptomycin. Recombinant human IL2 is added 24 hours later at a final concentration of 200 IU/ml and every three days thereafter with fresh media at 50 IU/ml. The cells are split if the cell concentration exceeds 1×10⁶/ml and the cultures are assayed between days 13 and 15 at E:T ratios of 30, 10, 3 and 1:1 in the ⁵¹Cr release assay or at 1×10⁶/ml in the in situ IFNγ assay using the same targets as before the expansion.

Cultures are expanded in the absence of anti-CD3⁺ as follows. Those cultures that demonstrate specific lytic activity against peptide and endogenous targets are selected and 5×10⁴ CD8⁺ cells are added to a T25 flask containing the following: 1×10⁶ autologous PBMC per ml which have been peptide-pulsed with 10 μg/ml peptide for two hours at 37° C. and irradiated (4,200 rad); 2×10⁵ irradiated (8,000 rad) EBV-transformed cells per ml RPMI-1640 containing 10% (v/v) human AB serum, non-essential AA, sodium pyruvate, 25 mM 2-ME, L-glutamine and gentamicin.

Immunogenicity of A2 Supermotif-Bearing Peptides

A2-supermotif cross-reactive binding peptides are tested in the cellular assay for the ability to induce peptide-specific CTL in normal individuals. In this analysis, a peptide is typically considered to be an epitope if it induces peptide-specific CTLs in at least individuals, and preferably, also recognizes the endogenously expressed peptide.

Immunogenicity can also be confirmed using PBMCs isolated from patients bearing a tumor that expresses 108P5H8. Briefly, PBMCs are isolated from patients, re-stimulated with peptide-pulsed monocytes and assayed for the ability to recognize peptide-pulsed target cells as well as transfected cells endogenously expressing the antigen.

Evaluation of A*03/A11 Immunogenicity

HLA-A3 supermotif-bearing cross-reactive binding peptides are also evaluated for immunogenicity using methodology analogous for that used to evaluate the immunogenicity of the HLA-A2 supermotif peptides.

Evaluation of B7 Immunogenicity

Immunogenicity screening of the B7-supertype cross-reactive binding peptides identified as set forth herein are confirmed in a manner analogous to the confirmation of A2-and A3-supermotif-bearing peptides.

Peptides bearing other supermotifs/motifs, e.g., HLA-A1, HLA-A24 etc. are also confirmed using similar methodology

Example 13 Implementation of the Extended Supermotif to Improve the Binding Capacity of Native Epitopes by Creating Analogs

HLA motifs and supermotifs (comprising primary and/or secondary residues) are useful in the identification and preparation of highly cross-reactive native peptides, as demonstrated herein. Moreover, the definition of HLA motifs and supermotifs also allows one to engineer highly cross-reactive epitopes by identifying residues within a native peptide sequence which can be analoged to confer upon the peptide certain characteristics, e.g. greater cross-reactivity within the group of HLA molecules that comprise a supertype, and/or greater binding affinity for some or all of those HLA molecules. Examples of analoging peptides to exhibit modulated binding affinity are set forth in this example.

Analoging at Primary Anchor Residues

Peptide engineering strategies are implemented to further increase the cross-reactivity of the epitopes. For example, the main anchors of A2-supermotif-bearing peptides are altered, for example, to introduce a preferred L, I, V, or M at position 2, and I or V at the C-terminus.

To analyze the cross-reactivity of the analog peptides, each engineered analog is initially tested for binding to the prototype A2 supertype allele A*0201, then, if A*0201 binding capacity is maintained, for A2-supertype cross-reactivity.

Alternatively, a peptide is confirmed as binding one or all supertype members and then analoged to modulate binding affinity to any one (or more) of the supertype members to add population coverage.

The selection of analogs for immunogenicity in a cellular screening analysis is typically further restricted by the capacity of the parent wild type (WT) peptide to bind at least weakly, i.e., bind at an IC₅₀ of 5000 nM or less, to three of more A2 supertype alleles. The rationale for this requirement is that the WT peptides must be present endogenously in sufficient quantity to be biologically relevant. Analoged peptides have been shown to have increased immunogenicity and cross-reactivity by T cells specific for the parent epitope (see, e.g., Parkhurst et al., J. Immunol. 157:2539, 1996; and Pogue et al., Proc. Natl. Acad. Sci. USA 92:8166, 1995).

In the cellular screening of these peptide analogs, it is important to confirm that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, target cells that endogenously express the epitope.

Analoging of HLA-A3 and B7-Supermotif-Bearing Peptides

Analogs of HLA-A3 supermotif-bearing epitopes are generated using strategies similar to those employed in analoging HLA-A2 supermotif-bearing peptides. For example, peptides binding to ⅗ of the A3-supertype molecules are engineered at primary anchor residues to possess a preferred residue (V, S, M, or A) at position 2.

The analog peptides are then tested for the ability to bind A*03 and A*11 (prototype A3 supertype alleles). Those peptides that demonstrate ≦500 nM binding capacity are then confirmed as having A3-supertype cross-reactivity.

Similarly to the A2- and A3-motif bearing peptides, peptides binding 3 or more B7-supertype alleles can be improved, where possible, to achieve increased cross-reactive binding or greater binding affinity or binding half life. B7 supermotif-bearing peptides are, for example, engineered to possess a preferred residue (V, I, L, or F) at the C-terminal primary anchor position, as demonstrated by Sidney et al. (J. Immunol. 157:3480-3490, 1996).

Analoging at primary anchor residues of other motif and/or supermotif-bearing epitopes is performed in a like manner.

The analog peptides are then be confirmed for immunogenicity, typically in a cellular screening assay. Again, it is generally important to demonstrate that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, targets that endogenously express the epitope.

Analoging at Secondary Anchor Residues

Moreover, HLA supermotifs are of value in engineering highly cross-reactive peptides and/or peptides that bind HLA molecules with increased affinity by identifying particular residues at secondary anchor positions that are associated with such properties. For example, the binding capacity of a B7 supermotif-bearing peptide with an F residue at position 1 is analyzed. The peptide is then analoged to, for example, substitute L for F at position 1. The analoged peptide is evaluated for increased binding affinity, binding half life and/or increased cross-reactivity. Such a procedure identifies analoged peptides with enhanced properties.

Engineered analogs with sufficiently improved binding capacity or cross-reactivity can also be tested for immunogenicity in HLA-B7-transgenic mice, following for example, IFA immunization or lipopeptide immunization. Analoged peptides are additionally tested for the ability to stimulate a recall response using PBMC from patients with 108P5H8-expressing tumors.

Other Analoging Strategies

Another form of peptide analoging, unrelated to anchor positions, involves the substitution of a cysteine with α-amino butyric acid. Due to its chemical nature, cysteine has the propensity to form disulfide bridges and sufficiently alter the peptide structurally so as to reduce binding capacity. Substitution of α-amino butyric acid for cysteine not only alleviates this problem, but has been shown to improve binding and crossbinding capabilities in some instances (see, e.g., the review by Sette et al., In: Persistent Viral Infections, Eds. R. Ahmed and I. Chen, John Wiley & Sons, England, 1999).

Thus, by the use of single amino acid substitutions, the binding properties and/or cross-reactivity of peptide ligands for HLA supertype molecules can be modulated.

Example 14 Identification and Confirmation of 108P5H8-Derived Sequences with HLA-DR Binding Motifs

Peptide epitopes bearing an HLA class II supermotif or motif are identified and confirmed as outlined below using methodology similar to that described for HLA Class I peptides.

Selection of HLA-DR-Supermotif-Bearing Epitopes.

To identify 108P5H8-derived, HLA class II HTL epitopes, a 108P5H8 antigen is analyzed for the presence of sequences bearing an HLA-DR-motif or supermotif. Specifically, 15 -mer sequences are selected comprising a DR-supermotif, comprising a 9 -mer core, and three-residue N- and C-terminal flanking regions (15 amino acids total).

Protocols for predicting peptide binding to DR molecules have been developed (Southwood et al., J. Immunol. 160:3363-3373, 1998). These protocols, specific for individual DR molecules, allow the scoring, and ranking, of 9 -mer core regions. Each protocol not only scores peptide sequences for the presence of DR-supermotif primary anchors (i.e., at position 1 and position 6) within a 9 -mer core, but additionally evaluates sequences for the presence of secondary anchors. Using allele-specific selection tables (see, e.g., Southwood et al., ibid.), it has been found that these protocols efficiently select peptide sequences with a high probability of binding a particular DR molecule. Additionally, it has been found that performing these protocols in tandem, specifically those for DR1, DR4w4, and DR7, can efficiently select DR cross-reactive peptides.

The 108P5H8-derived peptides identified above are tested for their binding capacity for various common HLA-DR molecules. All peptides are initially tested for binding to the DR molecules in the primary panel: DR1, DR4w4, and DR7. Peptides binding at least two of these three DR molecules are then tested for binding to DR2w2 β1, DR2w2 β2, DR6w19, and DR9 molecules in secondary assays. Finally, peptides binding at least two of the four secondary panel DR molecules, and thus cumulatively at least four of seven different DR molecules, are screened for binding to DR4w15, DR5w11, and DR8w2 molecules in tertiary assays. Peptides binding at least seven of the ten DR molecules comprising the primary, secondary, and tertiary screening assays are considered cross-reactive DR binders. 108P5H8-derived peptides found to bind common HLA-DR alleles are of particular interest.

Selection of DR3 Motif Peptides

Because HLA-DR3 is an allele that is prevalent in Caucasian, Black, and Hispanic populations, DR3 binding capacity is a relevant criterion in the selection of HTL epitopes. Thus, peptides shown to be candidates may also be assayed for their DR3 binding capacity. However, in view of the binding specificity of the DR3 motif, peptides binding only to DR3 can also be considered as candidates for inclusion in a vaccine formulation.

To efficiently identify peptides that bind DR3, target 108P5H8 antigens are analyzed for sequences carrying one of the two DR3-specific binding motifs reported by Geluk et al. (J. Immunol. 152:5742-5748, 1994). The corresponding peptides are then synthesized and confirmed as having the ability to bind DR3 with an affinity of 1 μM or better, i.e., less than 1 μM. Peptides are found that meet this binding criterion and qualify as HLA class II high affinity binders.

DR3 binding epitopes identified in this manner are included in vaccine compositions with DR supermotif-bearing peptide epitopes.

Similarly to the case of HLA class I motif-bearing peptides, the class II motif-bearing peptides are analoged to improve affinity or cross-reactivity. For example, aspartic acid at position 4 of the 9 -mer core sequence is an optimal residue for DR3 binding, and substitution for that residue often improves DR 3 binding.

Example 15 Immunogenicity of 108P5H8-Derived HTL Epitopes

This example determines immunogenic DR supermotif- and DR3 motif-bearing epitopes among those identified using the methodology set forth herein.

Immunogenicity of HTL epitopes are confirmed in a manner analogous to the determination of immunogenicity of CTL epitopes, by assessing the ability to stimulate HTL responses and/or by using appropriate transgenic mouse models. Immunogenicity is determined by screening for: 1.) in vitro primary induction using normal PBMC or 2.) recall responses from patients who have 108P5H8-expressing tumors.

Example 16 Calculation of Phenotypic Frequencies of HLA-Supertypes in Various Ethnic Backgrounds to Determine Breadth of Population Coverage

This example illustrates the assessment of the breadth of population coverage of a vaccine composition comprised of multiple epitopes comprising multiple supermotifs and/or motifs.

In order to analyze population coverage, gene frequencies of HLA alleles are determined. Gene frequencies for each HLA allele are calculated from antigen or allele frequencies utilizing the binomial distribution formulae gf=1−(SQRT(1−af)) (see, e.g., Sidney et al., Human Immunol. 45:79-93, 1996). To obtain overall phenotypic frequencies, cumulative gene frequencies are calculated, and the cumulative antigen frequencies derived by the use of the inverse formula [af=1−(1−Cgf)²].

Where frequency data is not available at the level of DNA typing, correspondence to the serologically defined antigen frequencies is assumed. To obtain total potential supertype population coverage no linkage disequilibrium is assumed, and only alleles confirmed to belong to each of the supertypes are included (minimal estimates). Estimates of total potential coverage achieved by inter-loci combinations are made by adding to the A coverage the proportion of the non-A covered population that could be expected to be covered by the B alleles considered (e.g., total=A+B*(1−A)). Confirmed members of the A3-like supertype are A3, A11, A31, A*3301,and A*6801. Although the A3-like supertype may also include A34, A66, and A*7401, these alleles were not included in overall frequency calculations. Likewise, confirmed members of the A2-like supertype family are A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*6802, and A*6901. Finally, the B7-like supertype-confirmed alleles are: B7, B*3501-03, B51, B*5301, B*5401,B*5501-2, B*5601, B*6701, and B*7801 (potentially also B*1401, B*3504-06, B*4201, and B*5602).

Population coverage achieved by combining the A2-, A3- and B7-supertypes is approximately 86% in five major ethnic groups. Coverage may be extended by including peptides bearing the A1 and A24 motifs. On average, Al is present in 12% and A24 in 29% of the population across five different major ethnic groups (Caucasian, North American Black, Chinese, Japanese, and Hispanic). Together, these alleles are represented with an average frequency of 39% in these same ethnic populations. The total coverage across the major ethnicities when A1 and A24 are combined with the coverage of the A2-, A3- and B7-supertype alleles is >95%. An analogous approach can be used to estimate population coverage achieved with combinations of class II motif-bearing epitopes.

Immunogenicity studies in humans (e.g., Bertoni et al., J. Clin. Invest. 100:503, 1997; Doolan et al., Immunity 7:97, 1997; and Threlkeld et al., J. Immunol. 159:1648, 1997) have shown that highly cross-reactive binding peptides are almost always recognized as epitopes. The use of highly cross-reactive binding peptides is an important selection criterion in identifying candidate epitopes for inclusion in a vaccine that is immunogenic in a diverse population.

With a sufficient number of epitopes (as disclosed herein and from the art), an average population coverage is predicted to be greater than 95% in each of five major ethnic populations. The game theory Monte Carlo simulation analysis, which is known in the art (see e.g., Osborne, M. J. and Rubinstein, A. “A course in game theory” MIT Press, 1994), can be used to estimate what percentage of the individuals in a population comprised of the Caucasian, North American Black, Japanese, Chinese, and Hispanic ethnic groups would recognize the vaccine epitopes described herein. A preferred percentage is 90%. A more preferred percentage is 95%.

Example 17 CTL Recognition of Endogenously Processed Antigens After Priming

This example confirms that CTL induced by native or analoged peptide epitopes identified and selected as described herein recognize endogenously synthesized, i.e., native antigens.

Effector cells isolated from transgenic mice that are immunized with peptide epitopes, for example HLA-A2 supermotif-bearing epitopes, are re-stimulated in vitro using peptide-coated stimulator cells. Six days later, effector cells are assayed for cytotoxicity and the cell lines that contain peptide-specific cytotoxic activity are further re-stimulated. An additional six days later, these cell lines are tested for cytotoxic activity on 51Cr labeled Jurkat-A2.1/K^(b) target cells in the absence or presence of peptide, and also tested on ⁵¹Cr labeled target cells bearing the endogenously synthesized antigen, i.e. cells that are stably transfected with 108P5H8 expression vectors.

The results demonstrate that CTL lines obtained from animals primed with peptide epitope recognize endogenously synthesized 108P5H8 antigen. The choice of transgenic mouse model to be used for such an analysis depends upon the epitope(s) that are being evaluated. In addition to HLA-A*0201/K^(b) transgenic mice, several other transgenic mouse models including mice with human A11, which may also be used to evaluate A3 epitopes, and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed, which may be used to evaluate HTL epitopes.

Example 18 Activity of CTL-HTL Conjugated Epitopes in Transgenic Mice

This example illustrates the induction of CTLs and HTLs in transgenic mice, by use of a 108P5H8-derived CTL and HTL peptide vaccine compositions. The vaccine composition used herein comprise peptides to be administered to a patient with a 108P5H8-expressing tumor. The peptide composition can comprise multiple CTL and/or HTL epitopes. The epitopes are identified using methodology as described herein. This example also illustrates that enhanced immunogenicity can be achieved by inclusion of one or more HTL epitopes in a CTL vaccine composition; such a peptide composition can comprise an HTL epitope conjugated to a CTL epitope. The CTL epitope can be one that binds to multiple HLA family members at an affinity of 500 nM or less, or analogs of that epitope. The peptides may be lipidated, if desired.

Immunization procedures. Immunization of transgenic mice is performed as described (Alexander et al., J. Immunol. 159:4753-4761, 1997). For example, A2/K^(b) mice, which are transgenic for the human HLA A2.1 allele and are used to confirm the immunogenicity of HLA-A*0201 motif- or HLA-A2 supermotif-bearing epitopes, and are primed subcutaneously (base of the tail) with a 0.1 ml of peptide in Incomplete Freund's Adjuvant, or if the peptide composition is a lipidated CTL/HTL conjugate, in DMSO/saline, or if the peptide composition is a polypeptide, in PBS or Incomplete Freund's Adjuvant. Seven days after priming, splenocytes obtained from these animals are restimulated with syngenic irradiated LPS-activated lymphoblasts coated with peptide.

Cell lines. Target cells for peptide-specific cytotoxicity assays are Jurkat cells transfected with the HLA-A2.1/K^(b) chimeric gene (e.g., Vitiello et al., J. Exp. Med. 173:1007, 1991)

In vitro CTL activation: One week after priming, spleen cells (30×10⁶ cells/flask) are co-cultured at 37° C. with syngeneic, irradiated (3000 rads), peptide coated lymphoblasts (10×10⁶ cells/flask) in 10 ml of culture medium/T25 flask. After six days, effector cells are harvested and assayed for cytotoxic activity.

Assay for cytotoxic activity: Target cells (1.0 to 1.5×10⁶) are incubated at 37° C. in the presence of 200 μl of ⁵¹Cr. After 60 minutes, cells are washed three times and resuspended in R10 medium. Peptide is added where required at a concentration of 1 μg/ml. For the assay, 10⁴ ⁵¹Cr-labeled target cells are added to different concentrations of effector cells (final volume of 200 μl) in U-bottom 96-well plates. After a six hour incubation period at 37° C., a 0.1 ml aliquot of supernatant is removed from each well and radioactivity is determined in a Micromedic automatic gamma counter. The percent specific lysis is determined by the formula: percent specific release=100× (experimental release−spontaneous release)/(maximum release−spontaneous release). To facilitate comparison between separate CTL assays run under the same conditions, % ⁵¹Cr release data is expressed as lytic units/10⁶ cells. One lytic unit is arbitrarily defined as the number of effector cells required to achieve 30% lysis of 10,000 target cells in a six hour ⁵¹Cr release assay. To obtain specific lytic units/10⁶, the lytic units/10⁶ obtained in the absence of peptide is subtracted from the lytic units/10⁶ obtained in the presence of peptide. For example, if 30% ⁵¹Cr release is obtained at the effector (E): target (T) ratio of 50:1 (i.e., 5×10⁵ effector cells for 10,000 targets) in the absence of peptide and 5:1 (i.e., 5×10⁴ effector cells for 10,000 targets) in the presence of peptide, the specific lytic units would be: [( 1/50,000)−( 1/500,000)]×10⁶=18 LU.

The results are analyzed to assess the magnitude of the CTL responses of animals injected with the immunogenic CTL/HTL conjugate vaccine preparation and are compared to the magnitude of the CTL response achieved using, for example, CTL epitopes as outlined above in the Example entitled “Confirmation of Immunogenicity”. Analyses similar to this may be performed to confirm the immunogenicity of peptide conjugates containing multiple CTL epitopes and/or multiple HTL epitopes. In accordance with these procedures, it is found that a CTL response is induced, and concomitantly that an HTL response is induced upon administration of such compositions.

Example 19 Selection of CTL and HTL Epitopes for Inclusion in an 108P5H8-Specific Vaccine

This example illustrates a procedure for selecting peptide epitopes for vaccine compositions of the invention. The peptides in the composition can be in the form of a nucleic acid sequence, either single or one or more sequences (i.e., minigene) that encodes peptide(s), or can be single and/or polyepitopic peptides.

The following principles are utilized when selecting a plurality of epitopes for inclusion in a vaccine composition. Each of the following principles is balanced in order to make the selection.

Epitopes are selected which, upon administration, mimic immune responses that are correlated with 108P5H8 clearance. The number of epitopes used depends on observations of patients who spontaneously clear 108P5H8. For example, if it has been observed that patients who spontaneously clear 108P5H8 generate an immune response to at least three (3) from 108P5H8 antigen, then three or four (3-4) epitopes should be included for HLA class I. A similar rationale is used to determine HLA class II epitopes.

Epitopes are often selected that have a binding affinity of an IC₅₀ of 500 nM or less for an HLA class I molecule, or for class II, an IC₅₀ of 1000 nM or less; or HLA Class I peptides with high binding scores from the BIAS web site, at URL bimas.dcrt.nih.gov/.

In order to achieve broad coverage of the vaccine through out a diverse population, sufficient supermotif bearing peptides, or a sufficient array of allele-specific motif bearing peptides, are selected to give broad population coverage. In one embodiment, epitopes are selected to provide at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess breadth, or redundancy, of population coverage.

When creating polyepitopic compositions, or a minigene that encodes same, it is typically desirable to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same, as those employed when selecting a peptide comprising nested epitopes. For example, a protein sequence for the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. Epitopes may be nested or overlapping (i.e., frame shifted relative to one another). For example, with overlapping epitopes, two 9 -mer epitopes and one 10 -mer epitope can be present in a 10 amino acid peptide. Each epitope can be exposed and bound by an HLA molecule upon administration of such a peptide. A multi-epitopic, peptide can be generated synthetically, recombinantly, or via cleavage from the native source. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes. This embodiment provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that is presently unknown. Furthermore, this embodiment (absent the creating of any analogs) directs the immune response to multiple peptide sequences that are actually present in 108P5H8, thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing nucleic acid vaccine compositions. Related to this embodiment, computer programs can be derived in accordance with principles in the art, which identify in a target sequence, the greatest number of epitopes per sequence length.

A vaccine composition comprised of selected peptides, when administered, is safe, efficacious, and elicits an immune response similar in magnitude to an immune response that controls or clears cells that bear or overexpress 108P5H8.

Example 20 Construction of “Minigene” Multi-Epitope DNA Plasmids

This example discusses the construction of a minigene expression plasmid. Minigene plasmids may, of course, contain various configurations of B cell, CTL and/or HTL epitopes or epitope analogs as described herein.

A minigene expression plasmid typically includes multiple CTL and HTL peptide epitopes. In the present example, HLA-A2, -A3, -B7 supermotif-bearing peptide epitopes and HLA-A1 and -A24 motif-bearing peptide epitopes are used in conjunction with DR supermotif-bearing epitopes and/or DR3 epitopes. HLA class I supermotif or motif-bearing peptide epitopes derived 108P5H8, are selected such that multiple supermotifs/motifs are represented to ensure broad population coverage. Similarly, HLA class II epitopes are selected from 108P5H8 to provide broad population coverage, i.e. both HLA DR-1-4-7 supermotif-bearing epitopes and HLA DR-3 motif-bearing epitopes are selected for inclusion in the minigene construct. The selected CTL and HTL epitopes are then incorporated into a minigene for expression in an expression vector.

Such a construct may additionally include sequences that direct the HTL epitopes to the endoplasmic reticulum. For example, the Ii protein may be fused to one or more HTL epitopes as described in the art, wherein the CLIP sequence of the Ii protein is removed and replaced with an HLA class II epitope sequence so that HLA class II epitope is directed to the endoplasmic reticulum, where the epitope binds to an HLA class II molecules.

This example illustrates the methods to be used for construction of a minigene-bearing expression plasmid. Other expression vectors that may be used for minigene compositions are available and known to those of skill in the art.

The minigene DNA plasmid of this example contains a consensus Kozak sequence and a consensus murine kappa Ig-light chain signal sequence followed by CTL and/or HTL epitopes selected in accordance with principles disclosed herein. The sequence encodes an open reading frame fused to the Myc and His antibody epitope tag coded for by the pcDNA 3.1 Myc-His vector.

Overlapping oligonucleotides that can, for example, average about 70 nucleotides in length with 15 nucleotide overlaps, are synthesized and HPLC-purified. The oligonucleotides encode the selected peptide epitopes as well as appropriate linker nucleotides, Kozak sequence, and signal sequence. The final multiepitope minigene is assembled by extending the overlapping oligonucleotides in three sets of reactions using PCR. A Perkin/Elmer 9600 PCR machine is used and a total of 30 cycles are performed using the following conditions: 95° C. for 15 sec, annealing temperature (5° below the lowest calculated Tm of each primer pair) for 30 sec, and 72° C. for 1 min.

For example, a minigene is prepared as follows. For a first PCR reaction, 5 μg of each of two oligonucleotides are annealed and extended: In an example using eight oligonucleotides, i.e., four pairs of primers, oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100 μl reactions containing Pfu polymerase buffer (1×=10 mM KCL, 10 mM (NH4)₂SO₄, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO₄, 0.1% Triton X-100, 100 μg/ml BSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. The full-length dimer products are gel-purified, and two reactions containing the product of 1+2 and 3+4, and the product of 5+6 and 7+8 are mixed, annealed, and extended for 10 cycles. Half of the two reactions are then mixed, and 5 cycles of annealing and extension carried out before flanking primers are added to amplify the full length product. The full-length product is gel-purified and cloned into pCR-blunt (Invitrogen) and individual clones are screened by sequencing.

Example 21 The Plasmid Construct and the Degree to Which it Induces Immunogenicity

The degree to which a plasmid construct, for example a plasmid constructed in accordance with the previous Example, is able to induce immunogenicity is confirmed in vitro by determining epitope presentation by APC following transduction or transfection of the APC with an epitope-expressing nucleic acid construct. Such a study determines “antigenicity” and allows the use of human APC. The assay determines the ability of the epitope to be presented by the APC in a context that is recognized by a T cell by quantifying the density of epitope-HLA class I complexes on the cell surface. Quantitation can be performed by directly measuring the amount of peptide eluted from the APC (see, e.g., Sijts et al., J. Immunol. 156:683-692, 1996; Demotz et al., Nature 342:682-684, 1989); or the number of peptide-HLA class I complexes can be estimated by measuring the amount of lysis or lymphokine release induced by diseased or transfected target cells, and then determining the concentration of peptide necessary to obtain. equivalent levels of lysis or lymphokine release (see, e.g., Kageyama et al., J. Immunol. 154:567-576, 1995).

Alternatively, immunogenicity is confirmed through in vivo injections into mice and subsequent in vitro assessment of CTL and HTL activity, which are analyzed using cytotoxicity and proliferation assays, respectively, as detailed e.g., in Alexander et al., Immunity 1:751-761, 1994.

For example, to confirm the capacity of a DNA minigene construct containing at least one HLA-A2 supermotif peptide to induce CTLs in vivo, HLA-A2.1/K^(b) transgenic mice, for example, are immunized intramuscularly with 100 μg of naked cDNA. As a means of comparing the level of CTLs induced by cDNA immunization, a control group of animals is also immunized with an actual peptide composition that comprises multiple epitopes synthesized as a single polypeptide as they would be encoded by the minigene.

Splenocytes from immunized animals are stimulated twice with each of the respective compositions (peptide epitopes encoded in the minigene or the polyepitopic peptide), then assayed for peptide-specific cytotoxic activity in a ⁵¹Cr release assay. The results indicate the magnitude of the CTL response directed against the A2-restricted epitope, thus indicating the in vivo immunogenicity of the minigene vaccine and polyepitopic vaccine.

It is, therefore, found that the minigene elicits immune responses directed toward the HLA-A2 supermotif peptide epitopes as does the polyepitopic peptide vaccine. A similar analysis is also performed using other HLA-A3 and HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 and HLA-B7 motif or supermotif epitopes, whereby it is also found that the minigene elicits appropriate immune responses directed toward the provided epitopes.

To confirm the capacity of a class II epitope-encoding minigene to induce HTLs in vivo, DR transgenic mice, or for those epitopes that cross react with the appropriate mouse MHC molecule, I-A^(b)-restricted mice, for example, are immunized intramuscularly with 100 μg of plasmid DNA. As a means of comparing the level of HTLs induced by DNA immunization, a group of control animals is also immunized with an actual peptide composition emulsified in complete Freund's adjuvant. CD4+ T cells, i.e. HTLs, are purified from splenocytes of immunized animals and stimulated with each of the respective compositions (peptides encoded in the minigene). The HTL response is measured using a ³H-thymidine incorporation proliferation assay, (see, e.g., Alexander et al. Immunity 1:751-761, 1994). The results indicate the magnitude of the HTL response, thus demonstrating the in vivo immunogenicity of the minigene.

DNA minigenes, constructed as described in the previous Example, can also be confirmed as a vaccine in combination with a boosting agent using a prime boost protocol. The boosting agent can consist of recombinant protein (e.g., Barnett et al., Aids Res. and Human Retroviruses 14, Supplement 3:S299-S309, 1998) or recombinant vaccinia, for example, expressing a minigene or DNA encoding the complete protein of interest (see, e.g., Hanke et al., Vaccine 16:439-445, 1998; Sedegah et al., Proc. Natl. Acad. Sci USA 95:7648-53,1998; Hanke and McMichael, Immunol. Letters 66:177-181, 1999; and Robinson et al., Nature Med. 5:526-34, 1999).

For example, the efficacy of the DNA minigene used in a prime boost protocol is initially evaluated in transgenic mice. In this example, A2.1/K^(b) transgenic mice are immunized IM with 100 μg of a DNA minigene encoding the immunogenic peptides including at least one HLA-A2 supermotif-bearing peptide. After an incubation period (ranging from 3-9 weeks), the mice are boosted IP with 10⁷ pfu/mouse of a recombinant vaccinia virus expressing the same sequence encoded by the DNA minigene. Control mice are immunized with 100 μg of DNA or recombinant vaccinia without the minigene sequence, or with DNA encoding the minigene, but without the vaccinia boost. After an additional incubation period of two weeks, splenocytes from the mice are immediately assayed for peptide-specific activity in an ELISPOT assay. Additionally, splenocytes are stimulated in vitro with the A2-restricted peptide epitopes encoded in the minigene and recombinant vaccinia, then assayed for peptide-specific activity in an alpha, beta and/or gamma IFN ELISA.

It is found that the minigene utilized in a prime-boost protocol elicits greater immune responses toward the HLA-A2 supermotif peptides than with DNA alone. Such an analysis can also be performed using HLA-A11 or HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 or HLA-B7 motif or supermotif epitopes. The use of prime boost protocols in humans is described below in the Example entitled “Induction of CTL Responses Using a Prime Boost Protocol.”

Example 22 Peptide Composition for Prophylactic Uses

Vaccine compositions of the present invention can be used to prevent 108P5H8 expression in persons who are at risk for tumors that bear this antigen. For example, a polyepitopic peptide epitope composition (or a nucleic acid comprising the same) containing multiple CTL and HTL epitopes such as those selected in the above Examples, which are also selected to target greater than 80% of the population, is administered to individuals at risk for a 108P5H8-associated tumor.

For example, a peptide-based composition is provided as a single polypeptide that encompasses multiple epitopes. The vaccine is typically administered in a physiological solution that comprises an adjuvant, such as Incomplete Freunds Adjuvant. The dose of peptide for the initial immunization is from about 1 to about 50,000 μg, generally 100-5,000 μg, for a 70 kg patient. The initial administration of vaccine is followed by booster dosages at 4 weeks followed by evaluation of the magnitude of the immune response in the patient, by techniques that determine the presence of epitope-specific CTL populations in a PBMC sample. Additional booster doses are administered as required. The composition is found to be both safe and efficacious as a prophylaxis against 108P5H8-associated disease.

Alternatively, a composition typically comprising transfecting agents is used for the administration of a nucleic acid-based vaccine in accordance with methodologies known in the art and disclosed herein.

Example 23 Polyepitopic Vaccine Compositions Derived from Native 108P5H8 Sequences

A native 108P5H8 polyprotein sequence is analyzed, preferably using computer algorithms defined for each class I and/or class II supermotif or motif, to identify “relatively short” regions of the polyprotein that comprise multiple epitopes. The “relatively short” regions are preferably less in length than an entire native antigen. This relatively short sequence that contains multiple distinct or overlapping, “nested” epitopes is selected; it can be used to generate a minigene construct. The construct is engineered to express the peptide, which corresponds to the native protein sequence. The “relatively short” peptide is generally less than 250 amino acids in length, often less than 100 amino acids in length, preferably less than 75 amino acids in length, and more preferably less than 50 amino acids in length. The protein sequence of the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. As noted herein, epitope motifs may be nested or overlapping (i.e., frame shifted relative to one another). For example, with overlapping epitopes, two 9 -mer epitopes and one 10 -mer epitope can be present in a 10 amino acid peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes.

The vaccine composition will include, for example, multiple CTL epitopes from 108P5H8 antigen and at least one HTL epitope. This polyepitopic native sequence is administered either as a peptide or as a nucleic acid sequence which encodes the peptide. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide.

The embodiment of this example provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that is presently unknown. Furthermore, this embodiment (excluding an analoged embodiment) directs the immune response to multiple peptide sequences that are actually present in native 108P5H8, thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing peptide or nucleic acid vaccine compositions.

Related to this embodiment, computer programs are available in the art which can be used to identify in a target sequence, the greatest number of epitopes per sequence length.

Example 24 Polyepitopic Vaccine Compositions from Multiple Antigens

The 108P5H8 peptide epitopes of the present invention are used in conjunction with epitopes from other target tumor-associated antigens, to create a vaccine composition that is useful for the prevention or treatment of cancer that expresses 108P5H8 and such other antigens. For example, a vaccine composition can be provided as a single polypeptide that incorporates multiple epitopes from 108P5H8 as well as tumor-associated antigens that are often expressed with a target cancer associated with 108P5H8 expression, or can be administered as a composition comprising a cocktail of one or more discrete epitopes. Alternatively, the vaccine can be administered as a minigene construct or as dendritic cells which have been loaded with the peptide epitopes in vitro.

Example 25 Use of Peptides to Evaluate an Immune Response

Peptides of the invention may be used to analyze an immune response for the presence of specific antibodies, CTL or HTL directed to 108P5H8. Such an analysis can be performed in a manner described by Ogg et al., Science 279:2103-2106, 1998. In this Example, peptides in accordance with the invention are used as a reagent for diagnostic or prognostic purposes, not as an immunogen.

In this example highly sensitive human leukocyte antigen tetrameric complexes (“tetramers”) are used for a cross-sectional analysis of, for example, 108P5H8 HLA-A*0201-specific CTL frequencies from HLA A*0201-positive individuals at different stages of disease or following immunization comprising an 168P5H8 peptide containing an A*0201 motif. Tetrameric complexes are synthesized as described (Musey et al., N. Engl. J. Med. 337:1267, 1997). Briefly, purified HLA heavy chain (A*0201 in this example) and β2-microglobulin are synthesized by means of a prokaryotic expression system. The heavy chain is modified by deletion of the transmembrane-cytosolic tail and COOH-terminal addition of a sequence containing a BirA enzymatic biotinylation site. The heavy chain, β2-microglobulin, and peptide are refolded by dilution. The 45 -kD refolded product is isolated by fast protein liquid chromatography and then biotinylated by BirA in the presence of biotin (Sigma, St. Louis, Mo.), adenosine 5′ triphosphate and magnesium. Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, and the tetrameric product is concentrated to 1 mg/ml. The resulting product is referred to as tetramer-phycoerythrin.

For the analysis of patient blood samples, approximately one million PBMCs are centrifuged at 300 g for 5 minutes and resuspended in 50 μl of cold phosphate-buffered saline. Tri-color analysis is performed with the tetramer-phycoerythrin, along with anti-CD8-Tricolor, and anti-CD38. The PBMCs are incubated with tetramer and antibodies on ice for 36 to 60 min and then washed twice before formaldehyde fixation. Gates are applied to contain >99.98% of control samples. Controls for the tetramers include both A*0201-negative individuals and A*0201-positive non-diseased donors. The percentage of cells stained with the tetramer is then determined by flow cytometry. The results indicate the number of cells in the PBMC sample that contain epitope-restricted CTLs, thereby readily indicating the extent of immune response to the 108P5H8 epitope, and thus the status of exposure to 108P5H8, or exposure to a vaccine that elicits a protective or therapeutic response.

Example 26 Use of Peptide Epitopes to Evaluate Recall Responses

The peptide epitopes of the invention are used as reagents to evaluate T cell responses, such as acute or recall responses, in patients. Such an analysis may be performed on patients who have recovered from 108P5H8-associated disease or who have been vaccinated with an 108P5H8 vaccine.

For example, the class I restricted CTL response of persons who have been vaccinated may be analyzed. The vaccine may be any 108P5H8 vaccine. PBMC are collected from vaccinated individuals and HLA typed. Appropriate peptide epitopes of the invention that, optimally, bear supermotifs to provide cross-reactivity with multiple HLA supertype family members, are then used for analysis of samples derived from individuals who bear that HLA type.

PBMC from vaccinated individuals are separated on Ficoll-Histopaque density gradients (Sigma Chemical Co., St. Louis, Mo.), washed three times in HBSS (GIBCO Laboratories), resuspended in RPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2 mM), penicillin (50 U/ml), streptomycin (50 μg/ml), and Hepes (10 mM) containing 10% heat-inactivated human AB serum (complete RPMI) and plated using microculture formats. A synthetic peptide comprising an epitope of the invention is added at 10 μg/ml to each well and HBV core 128-140 epitope is added at 1 μg/ml to each well as a source of T cell help during the first week of stimulation.

In the microculture format, 4×10⁵ PBMC are stimulated with peptide in 8 replicate cultures in 96-well round bottom plate in 100 μl/well of complete RPMI. On days 3 and 10, 100 μl of complete RPMI and 20 U/ml final concentration of rIL-2 are added to each well. On day 7 the cultures are transferred into a 96-well flat-bottom plate and restimulated with peptide, rIL-2 and 10⁵ irradiated (3,000 rad) autologous feeder cells. The cultures are tested for cytotoxic activity on day 14. A positive CTL response requires two or more of the eight replicate cultures to display greater than 10% specific ⁵¹Cr release, based on comparison with non-diseased control subjects as previously described (Rehermarm, et al., Nature Med. 2:1104,1108, 1996; Rehermann et al., J. Clin. Invest. 97:1655-1665, 1996; and Rehermann et al. J. Clin. Invest. 98:1432-1440, 1996).

Target cell lines are autologous and allogeneic EBV-transformed B-LCL that are either purchased from the American Society for Histocompatibility and Immunogenetics (ASHI, Boston, Mass.) or established from the pool of patients as described (Guilhot, et al. J. Virol. 66:2670-2678, 1992).

Cytotoxicity assays are performed in the following manner. Target cells consist of either allogeneic HLA-matched or autologous EBV-transformed B lymphoblastoid cell line that are incubated overnight with the synthetic peptide epitope of the invention at 10 μM, and labeled with 100 μCi of ⁵¹Cr (Amersham Corp., Arlington Heights, Ill.) for 1 hour after which they are washed four times with HBSS.

Cytolytic activity is determined in a standard 4 -h, split well ⁵¹Cr release assay using U-bottomed 96 well plates containing 3,000 targets/well. Stimulated PBMC are tested at effector/target (E/T) ratios of 20-50:1 on day 14. Percent cytotoxicity is determined from the formula: 100× [(experimental release−spontaneous release)/maximum release−spontaneous release)]. Maximum release is determined by lysis of targets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis, Mo.). Spontaneous release is <25% of maximum release for all experiments.

The results of such an analysis indicate the extent to which HLA-restricted CTL populations have been stimulated by previous exposure to 108P5H8 or an 108P5H8 vaccine.

Similarly, Class II restricted HTL responses may also be analyzed. Purified PBMC are cultured in a 96-well flat bottom plate at a density of 1.5×10⁵ cells/well and are stimulated with 10 μg/ml synthetic peptide of the invention, whole 108P5H8 antigen, or PHA. Cells are routinely plated in replicates of 4-6 wells for each condition. After seven days of culture, the medium is removed and replaced with fresh medium containing 10 U/ml IL-2. Two days later, 1 μCi ³H-thymidine is added to each well and incubation is continued for an additional 18 hours. Cellular DNA is then harvested on glass fiber mats and analyzed for ³H-thymidine incorporation. Antigen-specific T cell proliferation is calculated as the ratio of ³H-thymidine incorporation in the presence of antigen divided by the ³H-thymidine incorporation in the absence of antigen.

Example 27 Induction of Specific CTL Response in Humans

A human clinical trial for an immunogenic composition comprising CTL and HTL epitopes of the invention is set up as an IND Phase I, dose escalation study and carried out as a randomized, double-blind, placebo-controlled trial. Such a trial is designed, for example, as follows:

A total of about 27 individuals are enrolled and divided into 3 groups:

-   -   Group I: 3 subjects are injected with placebo and 6 subjects are         injected with 5 μg of peptide composition;     -   Group II: 3 subjects are injected with placebo and 6 subjects         are injected with 50 μg peptide composition;     -   Group III: 3 subjects are injected with placebo and 6 subjects         are injected with 500 μg of peptide composition.

After 4 weeks following the first injection, all subjects receive a booster inoculation at the same dosage.

The endpoints measured in this study relate to the safety and tolerability of the peptide composition as well as its immunogenicity. Cellular immune responses to the peptide composition are an index of the intrinsic activity of this the peptide composition, and can therefore be viewed as a measure of biological efficacy. The following summarize the clinical and laboratory data that relate to safety and efficacy endpoints.

Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility.

Evaluation of Vaccine Efficacy: For evaluation of vaccine efficacy, subjects are bled before and after injection. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

The vaccine is found to be both safe and efficacious.

Example 28 Phase II Trials in Patients Expressing 108P5H8

Phase II trials are performed to study the effect of administering the CTL-HTL peptide compositions to patients having cancer that expresses 108P5H8. The main objectives of the trial are to determine an effective dose and regimen for inducing CTLs in cancer patients that express 108P5H8, to establish the safety of inducing a CTL and HTL response in these patients, and to see to what extent activation of CTLs improves the clinical picture of these patients, as manifested, e.g., by the reduction and/or shrinking of lesions. Such a study is designed, for example, as follows:

The studies are performed in multiple centers. The trial design is an open-label, uncontrolled, dose escalation protocol wherein the peptide composition is administered as a single dose followed six weeks later by a single booster shot of the same dose. The dosages are 50, 500 and 5,000 micrograms per injection. Drug-associated adverse effects (severity and reversibility) are recorded.

There are three patient groupings. The first group is injected with 50 micrograms of the peptide composition and the second and third groups with 500 and 5,000 micrograms of peptide composition, respectively. The patients within each group range in age from 21-65 and represent diverse ethnic backgrounds. All of them have a tumor that expresses 108P5H8.

Clinical manifestations or antigen-specific T-cell responses are monitored to assess the effects of administering the peptide compositions. The vaccine composition is found to be both safe and efficacious in the treatment of 108P5H8-associated disease.

Example 29 Induction of CTL Responses Using a Prime Boost Protocol

A prime boost protocol similar in its underlying principle to that used to confirm the efficacy of a DNA vaccine in transgenic mice, such as described above in the Example entitled “The Plasmid Construct and the Degree to Which It Induces Immunogenicity,” can also be used for the administration of the vaccine to humans. Such a vaccine regimen can include an initial administration of, for example, naked DNA followed by a boost using recombinant virus encoding the vaccine, or recombinant protein/polypeptide or a peptide mixture administered in an adjuvant.

For example, the initial immunization may be performed using an expression vector, such as that constructed in the Example entitled “Construction of ‘Minigene’ Multi-Epitope DNA Plasmids” in the form of naked nucleic acid administered IM (or SC or ID) in the amounts of 0.5-5 mg at multiple sites. The nucleic acid (0.1 to 1000 μg) can also be administered using a gene gun. Following an incubation period of 3-4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-10⁷ to 5×10⁹ pfu. An alternative recombinant virus, such as an MVA, canarypox, adenovirus, or adeno-associated virus, can also be used for the booster, or the polyepitopic protein or a mixture of the peptides can be administered. For evaluation of vaccine efficacy, patient blood samples are obtained before immunization as well as at intervals following administration of the initial vaccine and booster doses of the vaccine. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

Analysis of the results indicates that a magnitude of response sufficient to achieve a therapeutic or protective immunity against 108P5H8 is generated.

Example 30 Administration of Vaccine Compositions Using Dendritic Cells (DC)

Vaccines comprising peptide epitopes of the invention can be administered using APCs, or “professional” APCs such as DC. In this example, peptide-pulsed DC are administered to a patient to stimulate a CTL response in vivo. In this method, dendritic cells are isolated, expanded, and pulsed with a vaccine comprising peptide CTL and HTL epitopes of the invention. The dendritic cells are infused back into the patient to elicit CTL and HTL responses in vivo. The induced CTL and HTL then destroy or facilitate destruction, respectively, of the target cells that bear the 108P5H8 protein from which the epitopes in the vaccine are derived.

For example, a cocktail of epitope-comprising peptides is administered ex vivo to PBMC, or isolated DC therefrom. A pharmaceutical to facilitate harvesting of DC can be used, such as Progenipoietin™ (Monsanto, St. Louis, Mo.) or GM-CSF/IL-4. After pulsing the DC with peptides, and prior to reinfusion into patients, the DC are washed to remove unbound peptides.

As appreciated clinically, and readily determined by one of skill based on clinical outcomes, the number of DC reinfused into the patient can vary (see, e.g., Nature Med. 4:328, 1998; Nature Med. 2:52, 1996 and Prostate 32:272, 1997). Although 2-50×10⁶ DC per patient are typically administered, larger number of DC, such as 10⁷ or 10⁸ can also be provided. Such cell populations typically contain between 50-90% DC.

In some embodiments, peptide-loaded PBMC are injected into patients without purification of the DC. For example, PBMC generated after treatment with an agent such as Progenipoietin™ are injected into patients without purification of the DC. The total number of PBMC that are administered often ranges from 10⁸ to 10¹⁰. Generally, the cell doses injected into patients is based on the percentage of DC in the blood of each patient, as determined, for example, by immunofluorescence analysis with specific anti-DC antibodies. Thus, for example, if Progenipoietin™ mobilizes 2% DC in the peripheral blood of a given patient, and that patient is to receive 5×10⁶ DC, then the patient will be injected with a total of 2.5×10⁸ peptide-loaded PBMC. The percent DC mobilized by an agent such as Progenipoietin™ is typically estimated to be between 2-10%, but can vary as appreciated by one of skill in the art.

Ex Vivo Activation of CTL/HTL Responses

Alternatively, ex vivo CTL or HTL responses to 108P5H8 antigens can be induced by incubating, in tissue culture, the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of APC, such as DC, and immunogenic peptides. After an appropriate incubation time (typically about 7-28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cells, i.e., tumor cells.

Example 31 An Alternative Method of Identifying and Confirming Motif-Bearing Peptides

Another method of identifying and confirming motif-bearing peptides is to elute them from cells bearing defined MHC molecules. For example, EBV transformed B cell lines used for tissue typing have been extensively characterized to determine which HLA molecules they express. In certain cases these cells express only a single type of HLA molecule. These cells can be transfected with nucleic acids that express the antigen of interest, e.g. 108P5H8. Peptides produced by endogenous antigen processing of peptides produced as a result of transfection will then bind to HLA molecules within the cell and be transported and displayed on the cell's surface. Peptides are then eluted from the HLA molecules by exposure to mild acid conditions and their amino acid sequence determined, e.g., by mass spectral analysis (e.g., Kubo et al., J. Immunol. 152:3913, 1994). Because the majority of peptides that bind a particular HLA molecule are motif-bearing, this is an alternative modality for obtaining the motif-bearing peptides correlated with the particular HLA molecule expressed on the cell.

Alternatively, cell lines that do not express endogenous HLA molecules can be transfected with an expression construct encoding a single HLA allele. These cells can then be used as described, i.e., they can then be transfected with nucleic acids that encode 108P5H8 to isolate peptides corresponding to 108P5H8 that have been presented on the cell surface. Peptides obtained from such an analysis will bear motif(s) that correspond to binding to the single HLA allele that is expressed in the cell.

As appreciated by one in the art, one can perform a similar analysis on a cell bearing more than one HLA allele and subsequently determine peptides specific for each HLA allele expressed. Moreover, one of skill would also recognize that means other than transfection, such as loading with a protein antigen, can be used to provide a source of antigen to the cell.

Example 32 Complementary Polynucleotides

Sequences complementary to the 108P5H8-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring 108P5H8. Although use of oligonucleotides comprising from about 15 to 30 base pairs is described, essentially the same procedure is used with smaller or with larger sequence fragments. Appropriate oligonucleotides are designed using, e.g., OLIGO 4.06 software (National Biosciences) and the coding sequence of 108P5H8. To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5′ sequence and used to prevent promoter binding to the coding sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding to a 108P5H8-encoding transcript.

Example 33 Purification of Naturally-Occurring or Recombinant 108P5H8 Using 108P5H8 Specific Antibodies

Naturally occurring or recombinant 108P5H8 is substantially purified by immunoaffinity chromatography using antibodies specific for 108P5H8. An immunoaffinity column is constructed by covalently coupling anti-108P5H8 antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin is blocked and washed according to the manufacturer's instructions.

Media containing 108P5H8 are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of 108P5H8 (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/108P5H8 binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and GCR.P is collected.

Example 34 Identification of Molecules which Interact with 108P5H8

108P5H8, or biologically active fragments thereof, are labeled with 121 1 Bolton-Hunter reagent. (See, e.g., Bolton et al. (1973) Biochem. J. 133:529.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled 108P5H8, washed, and any wells with labeled 108P5H8 complex are assayed. Data obtained using different concentrations of 108P5H8 are used to calculate values for the number, affinity, and association of 108P5H8 with the candidate molecules.

Example 35 In Vivo Assay for 108P5H8 Tumor Growth Promotion

The effect of a 108P5H8 protein on tumor cell growth can be confirmed in vivo by gene overexpression in a variety of cancer cells such as those in Table I, including prostate, kidney, colon and bladder. For example, SCID mice can be injected SQ on each flank with 1×10⁶ prostate, kidney, colon or bladder cancer cells (such as PC3, DU145, SCaBER, UM-UC-3, HT1376, SK-CO, Caco, RT4, T24, Caki, A-498 and SW839 cells) containing tkNeo empty vector or 108P5H8.

At least two strategies can be used:

-   -   (1) Constitutive 108P5H8 expression under regulation of a         promoter such as a constitutive promoter obtained from the         genomes of viruses such as polyoma virus, fowlpox virus (UK         2,211,504 published 5 Jul. 1989), adenovirus (such as Adenovirus         2), bovine papilloma virus, avian sarcoma virus,         cytomegalovirus, a retrovirus, hepatitis-B virus and Simian         Virus 40 (SV40), or from heterologous mammalian promoters, e.g.,         the actin promoter or an immunoglobulin promoter, provided such         promoters are compatible with the host cell systems.     -   (2) Regulated expression under control of an inducible vector         system, such as ecdysone, tet, etc., can be used provided such         promoters are compatible with the host cell systems. Tumor         volume is then monitored at the appearance of palpable tumors or         by following serum markers such as PSA. Tumor development is         followed over time to validate that 108P5H8-expressing cells         grow at a faster rate and/or that tumors produced by         108P5H8-expressing cells demonstrate characteristics of altered         aggressiveness (e.g., enhanced metastasis, vascularization,         reduced responsiveness to chemotherapeutic drugs). Tumor volume         is evaluated by caliper measurements. Additionally, mice can be         implanted with the same cells orthotopically in the prostate,         bladder, colon or kidney to determine if 108P5H8 has an effect         on local growth, e.g., in the prostate, bladder, colon or kidney         or on the ability of the cells to metastasize, specifically to         lungs or lymph nodes (Saffran et al., Proc Natl Acad Sci U S A.         2001, 98: 2658; Fu, X., et al., Int. J. Cancer, 1991. 49:         938-939; Chang, S., et al, Anticancer Res., 1997, 17: 3239-3242;         Peralta, E. A., et al., J. Urol., 1999. 162: 1806-1811). For         instance, the orthotopic growth of PC3 and PC3-108P5H8 can be         compared in the prostate of SCID mice. Such experiments reveal         the effect of 108P5H8 on orthotopic tumor growth, metastasis         and/or angiogenic potential.

Furthermore, this assay is useful to confirm the inhibitory effect of candidate therapeutic compositions, such as for example, 108P5H8 antibodies or intrabodies, and 108P5H8 antisense molecules or ribozymes, or 108P5H8 directed small molecules, on cells that express a 108P5H8 protein.

Example 36 108P5H8 Monoclonal Antibody-Mediated Inhibition of Human Xenograft Tumors in Vivo

The significant expression of 108P5H8, in cancer tissues, together with its restricted expression in normal tissues along with its cell surface expression makes 108P5H8 an excellent target for antibody therapy. Similarly, 108P5H8 is a target for T cell-based immunotherapy. Thus, the therapeutic efficacy of anti-108P5H8 mAbs is evaluated, e.g., in human prostate cancer xenograft mouse models using androgen-independent LAPC-4 and LAPC-9 xenografts (Craft, N., et al., Cancer Res, 1999. 59(19): p. 5030-5036), prostate cancer cell lines transfected with 108P5H8 (such as PC3-108P5H8, DU145-108P5H8), in human kidney cancer xenografts (AGS-K3, AGS-K6),.kidney cancer metastases to lymph node (AGS-K6 met) xenografts, and kidney cancer cell lines transfected with 108P5H8 (769P-108P5H8, A498-108P5H8).

Antibody efficacy on tumor growth and metastasis formation is studied, e.g., in mouse subcutaneous or orthotopic prostate cancer xenograft models and mouse kidney xenograft models. The antibodies can be unconjugated, as discussed in this Example, or can be conjugated to a therapeutic modality, as appreciated in the art. Anti-108P5H8 mAbs inhibit formation of both the androgen-dependent LAPC-9 and androgen-independent PC3-108P5H8 tumor xenografts. Anti-108P5H8 mAbs also retard the growth of established orthotopic tumors and prolonged survival of tumor-bearing mice. These results indicate the utility of anti-108P5H8 mAbs in the treatment of local and advanced stages of, e.g., prostate cancer. (See, e.g., Saffran, D., et al., PNAS 10:1073-1078 ). These results indicate the use of anti-108P5H8 mAbs in the treatment of prostate cancer.

Administration of the anti-108P5H8 mAbs leads to retardation of established orthotopic tumor growth and inhibition of metastasis to distant sites, resulting in a significant prolongation in the survival of tumor-bearing mice. These studies indicate that 108P5H8 is an attractive target for immunotherapy and demonstrate the therapeutic use of anti-108P5H8 mAbs for the treatment of local and metastatic cancer. This example demonstrates that unconjugated 108P5H8 monoclonal antibodies are effective to inhibit the growth of human prostate tumor xenografts and human kidney xenografts grown in SCID mice.

Tumor Inhibition Using Multiple Unconjugated 108P5H8 mAbs

Materials and Methods

108P5H8 Monoclonal Antibodies:

Monoclonal antibodies are obtained against 108P5H8, such as described in the Example entitled “Generation of 108P5H8 Monoclonal Antibodies (mAbs)” or may be obtained commercially. The antibodies are characterized by ELISA, Western blot, FACS, and immunoprecipitation for their capacity to bind 108P5H8. Epitope mapping data for the anti-108P5H8 mAbs, as determined by ELISA and Western analysis, recognize epitopes on a 108P5H8 protein. Immunohistochemical analysis of cancer tissues and cells is performed with these antibodies.

The monoclonal antibodies are purified from ascites or hybridoma tissue culture supernatants by Protein-G Sepharose chromatography, dialyzed against PBS, filter sterilized, and stored at −20° C. Protein determinations are performed by a Bradford assay (Bio-Rad, Hercules, Calif.). A therapeutic monoclonal antibody or a cocktail comprising a mixture of individual monoclonal antibodies is prepared and used for the treatment of mice receiving subcutaneous or orthotopic injections of, e.g., LAPC-9 prostate tumor xenografts.

Cancer Xenografts and Cell Lines

The LAPC-9 xenograft, which expresses a wild-type androgen receptor and produces prostate-specific antigen (PSA), is passaged in 6- to 8-week-old male ICR-severe combined immunodeficient (SCID) mice (Taconic Farms) by s.c. trocar implant (Craft, N., et al., 1999, Cancer Res. 59:5030-5036). Single-cell suspensions of tumor cells are prepared as described in Craft, et al. The prostate carcinoma cell lines PC3 and DU145 (American Type Culture Collection) are maintained in RPMI supplemented with L-glutamine and 10% FBS, and the kidney carcinoma line A498 (American Type Culture Collection) is maintained in DMEM supplemented with L-glutamine and 10% FBS.

PC3-108P5H8, DU145-108P5H8 and A498-108P5H8 cell populations are generated by retroviral gene transfer as described in Hubert, R. S., et al., STEAP: A Prostate-specific Cell-surface Antigen Highly Expressed in Human Prostate Tumors, Proc Natl Acad Sci U S A, 1999. 96(25): p. 14523-14528. Anti-108P5H8 staining is detected by using, e.g., an FITC-conjugated goat anti-mouse antibody (Southern Biotechnology Associates) followed by analysis on a Coulter Epics-XL flow cytometer.

Xenograft Mouse Models.

Subcutaneous (s.c.) tumors are generated by injection of 1×10⁶ LAPC-9, PC3, PC3-108P5H8, DU145 or DU145-108P5H8 cells mixed at a 1:1 dilution with Matrigel (Collaborative Research) in the right flank of male SCID mice. To test antibody efficacy on tumor formation, i.p. antibody injections are started on the same day as tumor-cell injections. As a control, mice are injected with either purified mouse IgG (ICN) or PBS; or a purified monoclonal antibody that recognizes an irrelevant antigen not expressed in human cells. In preliminary studies, no difference is found between mouse IgG or PBS on tumor growth. Tumor sizes are determined by vernier caliper measurements, and the tumor volume is calculated as length×width×height. Mice with s.c. tumors greater than 1.5 cm in diameter are sacrificed. PSA levels are determined by using a PSA ELISA kit (Anogen, Mississauga, Ontario). Circulating levels of anti-108P5H8 mAbs are determined by a capture ELISA kit (Bethyl Laboratories, Montgomery, Tex.). (See, e.g., (Saffran, D., et al., PNAS 10:1073-1078 ).

Orthotopic prostate injections are performed under anesthesia by using ketamine/xylazine. For prostate orthotopic studies, an incision is made through the abdominal muscles to expose the bladder and seminal vesicles, which then are delivered through the incision to expose the dorsal prostate. LAPC-9 cells (5×10⁵ ) mixed with Matrigel are injected into each dorsal lobe in a 10 μl volume. To monitor tumor growth, mice are bled on a weekly basis for determination of PSA levels. The mice are segregated into groups for appropriate treatments, with anti-108P5H8 or control mAbs being injected i.p.

Anti-108P5H8 mAbs Inhibit Growth of 108P5H8-Expressing Xenograft-Cancer Tumors

The effect of anti-108P5H8 mAbs on tumor formation is tested by using orthotopic models, e.g., LAPC-9 orthotopic models. As compared with the s.c. tumor model, the orthotopic model, which requires injection of tumor cells directly in the mouse prostate or kidney, respectively, results in a local tumor growth, development of metastasis in distal sites, deterioration of mouse health, and subsequent death (Saffran, D., et al., PNAS supra; Fu, X., et al., Int J Cancer, 1992. 52(6): p. 987-90; Kubota, T., J Cell Biochem, 1994. 56(1): p. 4-8). The features make the orthotopic model more representative of human disease progression and allow for tracking of the therapeutic effect of mAbs on clinically relevant end points.

Accordingly, tumor cells are injected into the mouse prostate or kidney, and the mice are segregated into two groups and treated with either: a) 200-500 μg, of anti-108P5H8 Ab, b) PBS or c) control non-specific monoclonal antibody for two to five weeks.

As noted, a major advantage of the orthotopic prostate-cancer model is the ability to study the development of metastases. Formation of metastasis in mice bearing established orthotopic tumors is studied by IHC analysis on lung sections using an antibody against a prostate-specific cell-surface protein STEAP expressed at high levels in LAPC-9 xenografts (Hubert, R. S., et al., Proc Natl Acad Sci U S A, 1999. 96(25): p. 14523-14528).

Mice bearing established orthotopic LAPC-9 tumors are administered one to three injections per week of 500-1000 μg of either anti-108P5H8 mAb, control antibody or PBS two-to three times per week over a 4-8 week period. Mice in both groups are allowed to establish a high tumor burden (PSA levels greater than 300 ng/ml), to ensure a high frequency of metastasis formation in mouse lungs. Mice then are killed and their prostate/kidney and lungs are analyzed for the presence of tumor cells by IHC analysis.

These studies demonstrate a broad anti-tumor efficacy of anti-108P5H8 antibodies on initiation and/or progression of prostate and kidney cancer in xenograft mouse models. Anti-108P5H8 antibodies inhibit tumor formation of both androgen-dependent and androgen-independent prostate tumors as well as retarding the growth of already established tumors and prolong the survival of treated mice. Moreover, anti-108P5H8 mAbs demonstrate a dramatic inhibitory effect on the spread of local prostate tumor to distal sites, even in the presence of a large tumor burden. Similar therapeutic effects are seen in the kidney cancer model. Thus, anti-108P5H8 mAbs are efficacious-on major clinically relevant end points (tumor growth), prolongation of survival, and health.

Example 37 Therapeutic and Diagnostic Use of Anti-108P5H8 Antibodies in Humans

Anti-108P5H8 monoclonal antibodies are safely and effectively used for diagnostic, prophylactic, prognostic and/or therapeutic purposes in humans. Western blot and immunohistochemical analysis of cancer tissues and cancer xenografts with anti-108P5H8 mAb show strong extensive staining in carcinoma but significantly lower or undetectable levels in normal tissues. Detection of 108P5H8 in carcinoma and in metastatic disease demonstrates the usefulness of the mAb as a diagnostic and/or prognostic indicator. Anti-108P5H8 antibodies are therefore used in diagnostic applications such as immunohistochemistry of biopsy specimens to detect cancer from suspect patients.

As determined by immunofluorescence, anti-108P5H8 mAb specifically binds to carcinoma cells. Thus, anti-108P5H8 antibodies are used in diagnostic whole body imaging applications, such as radioimmunoscintigraphy and radioimmunotherapy, (see, e.g., Potamianos S., et. al. Anticancer Res 20(2A):925-948 (2000)) for the detection of localized and metastatic cancers that exhibit expression of 108P5H8. Shedding or release of an extracellular domain of 108P5H8 into the extracellular milieu, such as that seen for alkaline phosphodiesterase BIO (Meerson, N. R., Hepatology 27:563-568 (1998)), allows diagnostic detection of 108P5H8 by anti-108P5H8 antibodies in serum and/or urine samples from suspect patients.

Anti-108P5H8 antibodies that specifically bind 108P5H8 are used in therapeutic applications for the treatment of cancers that express 108P5H8. Anti-108P5H8 antibodies are used as an unconjugated modality and as conjugated form in which the antibodies are attached to one of various therapeutic or imaging modalities well known in the art, such as a prodrugs, enzymes or radioisotopes. In preclinical studies, unconjugated and conjugated anti-108P5H8 antibodies are tested for efficacy of tumor prevention and growth inhibition in the SCID mouse cancer xenograft models, e.g., LAPC9 (see, e.g., the Example entitled “Monoclonal Antibody-mediated Inhibition of Prostate and Kidney Tumors In vivo.”) Conjugated and unconjugated anti-108P5H8 antibodies are used as a therapeutic modality in human clinical trials either alone or in combination with other treatments as described in following Examples.

Example 38 Human Clinical Trials for the Treatment and Diagnosis of Human Carcinomas Through Use of Human Anti-108P5H8 Antibodies in Vivo

Antibodies are used in accordance with the present invention which recognize an epitope on 108P5H8, and are used in the treatment of certain tumors such as those listed in Table I. Based upon a number of factors, including 108P5H8 expression levels, tumors such as those listed in Table I are presently preferred indications. In connection with each of these indications, three clinical approaches are successfully pursued.

I.) Adjunctive therapy: In adjunctive therapy, patients are treated with anti-108P5H8 antibodies in combination with a chemotherapeutic or antineoplastic agent and/or radiation therapy. Primary cancer targets, such as those listed in Table I, are treated under standard protocols by the addition anti-108P5H8 antibodies to standard first and second line therapy. Protocol designs address effectiveness as assessed by reduction in tumor mass as well as the ability to reduce usual doses of standard chemotherapy. These dosage reductions allow additional and/or prolonged therapy by reducing dose-related toxicity of the chemotherapeutic agent. Anti-108P5H8 antibodies are utilized in several adjunctive clinical trials in combination with the chemotherapeutic or antineoplastic agents adriamycin (advanced prostrate carcinoma), cisplatin (advanced head and neck and lung carcinomas), taxol (breast cancer), and doxorubicin (preclinical).

II.) Monotherapy: In connection with the use of the anti-108P5H8 antibodies in monotherapy of tumors, the antibodies are administered to patients without a chemotherapeutic or antineoplastic agent. In one embodiment, monotherapy is conducted clinically in end stage cancer patients with extensive metastatic disease. Patients show some disease stabilization. Trials demonstrate an effect in refractory patients with cancerous tumors.

III.) Imaging Agent: Through binding a radionuclide (e.g., iodine or yttrium (I¹³¹, Y⁹⁰) to anti-108P5H8 antibodies, the radiolabeled antibodies are utilized as a diagnostic and/or imaging agent. In such a role, the labeled antibodies localize to both solid tumors, as well as, metastatic lesions of cells expressing 108P5H8. In connection with the use of the anti-108P5H8 antibodies as imaging agents, the antibodies are used as an adjunct to surgical treatment of solid tumors, as both a pre-surgical screen as well as a post-operative follow-up to determine what tumor remains and/or returns. In one embodiment, a (¹¹¹In)-108P5H8 antibody is used as an imaging agent in a Phase I human clinical trial in patients having a carcinoma that expresses 108P5H8 (by analogy see, e.g., Divgi et al. J. Natl. Cancer Inst. 83:97-104 (1991)). Patients are followed with standard anterior and posterior gamma camera. The results indicate that primary lesions and metastatic lesions are identified

Dose and Route of Administration

As appreciated by those of ordinary skill in the art, dosing considerations can be determined through comparison with the analogous products that are in the clinic. Thus, anti-108P5H8 antibodies can be administered with doses in the range of 5 to 400 mg/m², with the lower doses used, e.g., in connection with safety studies. The affinity of anti-108P5H8 antibodies relative to the affinity of a known antibody for its target is one parameter used by those of skill in the art for determining analogous dose regimens. Further, anti-108P5H8 antibodies that are fully human antibodies, as compared to the chimeric antibody, have slower clearance; accordingly, dosing in patients with such fully human anti-108P5H8 antibodies can be lower, perhaps in the range of 50 to 300 mg/m², and still remain efficacious. Dosing in mg/m², as opposed to the conventional measurement of dose in mg/kg, is a measurement based on surface area and is a convenient dosing measurement that is designed to include patients of all sizes from infants to adults.

Three distinct delivery approaches are useful for delivery of anti-108P5H8 antibodies. Conventional intravenous delivery is one standard delivery technique for many tumors. However, in connection with tumors in the peritoneal cavity, such as tumors of the ovaries, biliary duct, other ducts, and the like, intraperitoneal administration may prove favorable for obtaining high dose of antibody at the tumor and to also minimize antibody clearance. In a similar manner, certain solid tumors possess vasculature that is appropriate for regional perfusion. Regional perfusion allows for a high dose of antibody at the site of a tumor and minimizes short term clearance of the antibody.

Clinical Development Plan (CDP)

Overview: The CDP follows and develops treatments of anti-108P5H8 antibodies in connection with adjunctive therapy, monotherapy, and as an imaging agent. Trials initially demonstrate safety and thereafter confirm efficacy in repeat doses. Trails are open label comparing standard chemotherapy with standard therapy plus anti-108P5H8 antibodies. As will be appreciated, one criteria that can be utilized in connection with enrollment of patients is 108P5H8 expression levels in their tumors as determined by biopsy.

As with any protein or antibody infusion-based therapeutic, safety concerns are related primarily to (i) cytokine release syndrome, i.e., hypotension, fever, shaking, chills; (ii) the development of an immunogenic response to the material (i.e., development of human antibodies by the patient to the antibody therapeutic, or HAHA response); and, (iii) toxicity to normal cells that express 108P5H8. Standard tests and follow-up are utilized to monitor each of these safety concerns. Anti-108P5H8 antibodies are found to be safe upon human administration.

Example 39 Human Clinical Trial Adjunctive Therapy with Human Anti-108P5H8 Antibody and Chemotherapeutic Agent

A phase I human clinical trial is initiated to assess the safety of six intravenous doses of a human anti-108P5H8 antibody in connection with the treatment of a solid tumor, e.g., a cancer of a tissue listed in Table I. In the study, the safety of single doses of anti-108P5H8 antibodies when utilized as an adjunctive therapy to an antineoplastic or chemotherapeutic agent, such as cisplatin, topotecan, doxorubicin, adriamycin, taxol, or the like, is assessed. The trial design includes delivery of six single doses of an anti-108P5H8 antibody with dosage of antibody escalating from approximately about 25 mg/m²to about 275 mg/m² over the course of the treatment in accordance with the following schedule:

Day0 Day7 Day14 Day21 Day28 Day35 mAb Dose 25 75 125 175 225 275 mg/m² mg/m² mg/m² mg/m² mg/m² mg/m² Chemotherapy + + + + + + (standard dose)

Patients are closely followed for one-week following each administration of antibody and chemotherapy. In particular, patients are assessed for the safety concerns mentioned above: (i) cytokine release syndrome, i.e., hypotension, fever, shaking, chills; (ii) the development of an immunogenic response to the material (i.e., development of human antibodies by the patient to the human antibody therapeutic, or HAHA response); and, (iii) toxicity to normal cells that express 108P5H8. Standard tests and follow-up are utilized to monitor each of these safety concerns. Patients are also assessed for clinical outcome, and particularly reduction in tumor mass as evidenced by MRI or other imaging.

The anti-108P5H8 antibodies are demonstrated to be safe and efficacious, Phase II trials confirm the efficacy and refine optimum dosing.

Example 40 Human Clinical Trial: Monotherapy with Human Anti-108P5H8 Antibody

Anti-108P5H8 antibodies are safe in connection with the above-discussed adjunctive trial, a Phase II human clinical trial confirms the efficacy and optimum dosing for monotherapy. Such trial is accomplished, and entails the same safety and outcome analyses, to the above-described adjunctive trial with the exception being that patients do not receive chemotherapy concurrently with the receipt of doses of anti-108P5H8 antibodies.

Example 41 Human Clinical Trial: Diagnostic Imaging with Anti-108P5H8 Antibody

Once again, as the adjunctive therapy discussed above is safe within the safety criteria discussed above, a human clinical trial is conducted concerning the use of anti-108P5H8 antibodies as a diagnostic imaging agent. The protocol is designed in a substantially similar manner to those described in the art, such as in Divgi et al. J. Natl. Cancer Inst. 83:97-104 (1991). The antibodies are found to be both safe and efficacious when used as a diagnostic modality.

Example 42 Homology Comparison of 108P5H8 to Known Sequences

The 108P5H8 protein is a six-transmembrane type 3 cell surface protein, consisting of 429 amino acids (table XXI). The 108P5H8 protein has 2 variant forms (FIG. 3), with 108P5H8v.3 differing from 108P5H8 v.1 by one amino acid at position 30 (D to E). This alteration in amino acid at position 30 corresponds to a point mutation at nucleic acid position 90, making variant 3 a true SNP. Both 108P5H8 variants, 108P5H8 v.1 and 108P5H8 v.3 have a calculated molecular weight of 47.5 kDa, and pI of 6.11, and contain an ion efflux motif between amino acid 114-417. Proteins carrying the ion efflux motif are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells (Kunito T et al, Biosci Biotechnol Biochem 1996, 60:699).

The 108P5H8 protein variants show homology to human zinc transporter 4 (gi 11432533); with 108P5H8v.1 sharing 100% identity and 100% homology with that protein over the entire length of the protein (FIG. 25). 108P5H8v.2 share 100% identity and 100% homology with human zinc transporter ZNT4-gi 8134840 over the entire protein. As with the two 108P5H8 variants, ZNT4 (gi 8134840) and ZNT4-gi 11432533 differ by one amino acid at position 30, showing the same D to E change observed in 108P5H8v.3 and 108P5H8v.1. Based on sequence homology, 108P5H8 is conserved in various, species, showing high homology to Rat ZNT4 (90% identify shown in FIG. 25) and mouse ZNT4 (91% identity with gi 8134841).

Zinc has been shown to play an important role in the physiology and pathology of prostate epithelial cells. Zinc ions regulate the activity of chromatin and plasmalemma structures in seminal plasma, and participate in spermadhesin function (Holody D and Strzezek J. Acta Biochini Pol 1999, 46:935). In relation to prostate cancer, zinc was found to inhibit the activity of aminopeptidase N in prostate cancer cells (Ishii K et al, Int J Cancer 2001, 92:49). Efflux of Zn⁺⁺ from the prostate by 108P5H8 or ZNT4 enhances the endogenous activity of aminopeptidase N, thereby increasing matrix degradation and tissue invasion by prostate cancer cells. In addition to its role in invasion, ZNT4 regulates apoptosis and proliferation of prostate cells. Accumulation of Zn⁺⁺ within the prostate induces apoptosis of normal epithelial cells (Feng P et al, Mol Urol 2000, 4:31). Enhanced expression of ZNT4 in prostate cancer cells and the resulting efflux of Zn⁺⁺, allow reduced apoptosis, survival and proliferation of prostate cancer cells. Finally, intracellular Zn⁺⁺ concentrations play a direct role in regulating gene transcription by zinc finger proteins.

This information indicates that 108P5H8 plays a role in the growth of cancer cells, supports cell survival, and regulates gene transcription by regulating events in the nucleus. Accordingly, when 108P5H8 functions as a regulator of cell transformation, tumor formation, or as a modulator of transcription involved in activating genes associated with inflammation, tumorigenesis or proliferation, 108P5H8 is used for therapeutic, diagnostic, prognostic and/or preventative purposes.

Example 43 Identification and Confirmation of Signal Transduction Pathways

Many mammalian proteins have been reported to interact with signaling molecules and to participate in regulating signaling pathways. (see, e.g., J. Neurochem. 2001; 76:217-223). Using immunoprecipitation and Western blotting techniques, proteins are identified that associate with 108P5H8 and mediate signaling events. Several pathways known to play a role in cancer biology can be regulated by 108P5H8, including phospholipid pathways such as P13K, AKT, etc, adhesion and migration pathways, including FAK, Rho, Rac-1, etc, as well as mitogenic/survival cascades such as ERK, p38, etc. (Cell Growth Differ. 2000, 11:279; J. Biol. Chem. 1999, 274:801; Oncogene. 2000, 19:3003, J. Cell Biol. 1997, 138:913).

To confirm that 108P5H8 directly or indirectly activates known signal transduction pathways in cells, luciferase (luc) based transcriptional reporter assays are carried out in cells expressing individual genes. These transcriptional reporters contain consensus-binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways. The reporters and examples of these associated transcription factors, signal transduction pathways, and activation stimuli are listed below.

-   -   1. NFkB-luc, NFkB/Rel; Ik-kinase/SAPK; growth/apoptosis/stress     -   2. SRE-luc, SRF/TCF/ELK1; MAPK/SAPK; growth/differentiation     -   3. AP-1-luc, FOS/JUN; MAPK/SAPK/PKC; growth/apoptosis/stress     -   4. ARE-luc, androgen receptor; steroids/MAPK;         growth/differentiation/apoptosis     -   5. p53-luc, p53; SAPK; growth/differentiation/apoptosis     -   6. CRE-luc, CREB/ATF2; PKA/p38; growth/apoptosis/stress

Gene-mediated effects can be assayed in cells showing mRNA expression. Luciferase reporter plasmids can be introduced by lipid-mediated transfection (TFX-50, Promega). Luciferase activity, an indicator of relative transcriptional activity, is measured by incubation of cell extracts with luciferin substrate and luminescence of the reaction is monitored in a luminometer.

Signaling pathways activated by 108P5H8 are mapped and used for the identification and validation of therapeutic targets. When 108P5H8 is involved in cell signaling, it is used as target for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 44 Involvement in Tumor Progression

The 108P5H8 gene contributes to the growth of cancer cells. The role of 108P5H8 in tumor growth is confirmed in a variety of primary and transfected cell lines including prostate cell lines, as well as NIH 3T3 cells engineered to stably express 108P5H8. Parental cells lacking 108P5H8 and cells expressing 108P5H8 are evaluated for cell growth using a well-documented proliferation assay (Fraser, S. P., et al., Prostate 2000; 44:61, Johnson, D. E., et al., Anticancer Drugs 1996, 7:288).

To confirm the role of 108P5H8 in the transformation process, its effect in colony forming assays is investigated. Parental NIH-3T3 cells lacking 108P5H8 are compared to NIH-3T3 cells expressing 108P5H8, using a soft agar assay under stringent and more permissive conditions (Song, Z., et al., Cancer Res. 2000; 60:6730).

To confirm the role of 108P5H8 in invasion and metastasis of cancer cells, a well-established assay is used, e.g., a Transwell Insert System assay (Becton Dickinson) (Cancer Res. 1999; 59:6010). Control cells, including prostate, colon, bladder and kidney cell lines lacking 108P5H8 are compared to corresponding cells expressing 108P5H8. Cells are loaded with the fluorescent dye, calcein, and plated in the top well of the Transwell insert coated with a basement membrane analog. Invasion is determined by fluorescence of cells in the lower chamber relative to the fluorescence of the entire cell population.

108P5H8 can also play a role in cell cycle and apoptosis. Parental cells and cells expressing 108P5H8 are compared for differences in cell cycle regulation using a well-established BrdU assay (Abdel-Malek Z A., J Cell Physiol. 1988, 136:247). In short, cells are grown under both optimal (full serum) and limiting (low serum) conditions, labeled with BrdU and stained with anti-BrdU Ab and propidium iodide. Cells are analyzed for entry into the G1, S, and G2M phases of the cell cycle. Alternatively, the effect of stress on apoptosis is evaluated in control parental cells and cells expressing 108P5H8, including normal and tumor prostate, colon and lung cells. Engineered and parental cells are treated with various chemotherapeutic agents, such as etoposide, flutamide, etc., and protein synthesis inhibitors, such as cycloheximide. Cells are stained with annexin V-FITC and cell death is measured by FACS analysis. Modulation of cell death by 108P5H8 plays a critical role in regulating tumor progression and tumor load.

When 108P5H8 plays a role in cell growth, transformation, invasion or apoptosis, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 45 Involvement in Angiogenesis

Angiogenesis or new capillary blood vessel formation is necessary for tumor growth (Hanahan, D., Folkman, J., Cell 1996, 86:353; Folkman, J., Endocrinology 1998, 139:441). Several assays have been developed to measure angiogenesis in vitro and in vivo, such as the tissue culture assays endothelial cell tube formation and endothelial cell proliferation. Using these assays as well as in vitro neo-vascularization, the role of 108P5H8 in angiogenesis, enhancement or inhibition, is confirmed.

For example, endothelial cells engineered to express 108P5H8 are evaluated using tube formation and proliferation-assays. The effect of 108P5H8 is also confirmed in animal models in vivo. For example, cells either expressing or lacking 108P5H8 are implanted subcutaneously in immunocompromised mice. Endothelial cell migration and angiogenesis are evaluated 5-15 days later using immunohistochemistry techniques. 108P5H8 affects angiogenesis, and it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes

Example 46 Regulation of Transcription

The cellular localization of 108P5H8 (Table XXI) and its ability to regulate intracellular zinc ion concentrations, 108P5H8 is effectively used as a modulator of the transcriptional regulation of eukaryotic genes. Regulation of gene expression is confirmed, e.g., by studying gene expression in cells expressing or lacking 108P5H8. For this purpose, two types of experiments are performed.

In the first set of experiments, RNA from parental and 108P5H8-expressing cells are extracted and hybridized to commercially available gene arrays (Clontech) (Smid-Koopman, E., et al., Br. J. Cancer, 2000, 83:246). Resting cells as well as cells treated with FBS or androgen are compared. Differentially expressed genes are identified in accordance with procedures known in the art. The differentially expressed genes are then mapped to biological pathways (Chen, K., et al. Thyroid 2001, 11:41.).

In the second set of experiments, specific transcriptional pathway activation is evaluated using commercially available (Stratagene) luciferase reporter constructs including: NFkB-luc, SRE-luc, ELK1-luc, ARE-luc, p53-luc, and CRE-luc. These transcriptional reporters contain consensus binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways, and represent a good tool to ascertain pathway activation and screen for positive and negative modulators of pathway activation.

Accordingly, it is found that 108P5H8 plays a role in gene regulation, and it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 47 Involvement in Cell Adhesion

Cell adhesion plays a critical role in tissue colonization and metastasis. 108P5H8 participates in cellular organization, and as a consequence cell adhesion and motility. To confirm the role of 108P5H8 in the regulation of cell adhesion, control cells lacking 108P5H8 are compared to cells expressing 108P5H8, using techniques previously described (see, e.g., Haier et al., Br. J. Cancer, 1999, 80:1867; Lehr and Pienta, J. Natl. Cancer Inst. 1998, 90:118). Briefly, in one embodiment, cells labeled with a fluorescent indicator, such as calcein, are incubated in tissue culture wells coated with media alone or with matrix proteins. Adherent cells are detected by fluorimetric analysis and percent adhesion is calculated. In another embodiment, cells lacking or expressing 108P5H8 are analyzed for their ability to mediate cell-cell adhesion using similar experimental techniques as described above. Both of these experimental systems are used to identify proteins, antibodies and/or small molecules that modulate cell adhesion to extracellular matrix and cell-cell interaction. Cell adhesion plays a critical role in tumor growth, progression, and, colonization, and 108P5H8 is involved in these processes. Thus, 108P5H8 serves as a diagnostic, prognostic, preventative and/or therapeutic modality.

Example 48 Protein-Protein Association

Several ion transporters have been shown to interact with other proteins, thereby regulating gene transcription, gene sequence, as well as cell growth. Using immunoprecipitation techniques as well as two yeast hybrid systems, proteins are identified that associate with 108P5H8. Immunoprecipitates from cells expressing 108P5H8 and cells lacking 108P5H8 are compared for specific protein-protein associations.

Studies are performed to confirm the extent of association of 108P5H8 with effector molecules, such as nuclear proteins, transcription factors, kinases, phsophates, etc. Studies comparing 108P5H8 positive and 108P5H8 negative cells as well as studies comparing unstimulated/resting cells and cells treated with epithelial cell activators, such as cytokines, growth factors, androgen and anti-integrin Ab reveal unique interactions.

In addition, protein-protein interactions are confirmed using two yeast hybrid methodology (Curr. Opin. Chem. Biol. 1999, 3:64). A vector carrying a library of proteins fused to the activation domain of a transcription factor is introduced into yeast expressing a 108P5H8-DNA-binding domain fusion protein and a reporter construct. Protein-protein interaction is detected by colorimetric reporter activity. Specific association with effector molecules and transcription factors directs one of skill to the mode of action of 108P5H8, and thus identifies therapeutic, prognostic, preventative and/or diagnostic targets for cancer. This and similar assays are also used to identify and screen for small molecules that interact with 108P5H8.

Thus it is found that 108P5H8 associates with proteins and small molecules. Accordingly, 108P5H8 and these proteins and small molecules are used for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 49 Ion Flux Activity

To confirm that 108P5H8 functions as an ion channel, FACS analysis and electrophysiology techniques are used (Gergely L, Cook L, Agnello V. Clin Diagn Lab Immunol. 1997;4:70; Skryma R, et al. J Physiol. 2000, 527: 71). Using FACS analysis and commercially available indicators (Molecular Probes), parental cells and cells expressing genes under consideration are compared for their ability to transport calcium, and zinc. Prostate, colon, bladder and kidney normal and tumor cell lines are used in these studies. For example cells loaded with calcium responsive indicators such as Fluo4 and Fura red are incubated in the presence or absence of ions and analyzed by flow cytometry. Information derived from these experiments provides a mechanism by which cancer cells are regulated. This is particularly true in the case of calcium, as calcium channel inhibitors have been reported to induce the death of certain cancer cells, including prostate cancer cell lines (Batra S, Popper L D, Hartley-Asp B. Prostate. 1991, 19: 299). It is possible to determine efflux and influx of zinc using fluoZin 1, a fluorescent Zn⁺⁺ indicator detected by FACS in a manner similar to Fluo4 above, or using ⁶⁵Zn. Prostate, kidney, bladder or colon cells, engineered to express or lack 108P5H8, will be incubated in the presence of ⁶⁵Zn. Cells will be evaluated over time for uptake and efflux of ⁶⁵Zn (Kim A H et al, Brain Res. 2000, 886:99; Grass G et al, J Bacteriol. 2001, 183:4664).

Using electrophysiology, uninjected oocytes and oocytes injected with gene-specific cRNA are compared for ion channel activity. Patch/voltage clamp assays are performed on oocytes in the presence or absence of selected ions, including calcium, zinc, etc. Ion channel activators (such as cAMP/GMP, forskolin, TPA, etc) and inhibitors (such as calcicludine, conotoxin, TEA, tetrodotoxin, etc) are used to evaluate the function of 108P5H8 as ion channels (Schweitz H. et al. Proc. Natl. Acad. Sci. 1994. 91:878; Skryma R. et al. Prostate. 1997. 33:112).

Using any of the assays listed above, we can evaluate the effect of antibodies directed against 108P5H8 on ion transport. Similarly, these assays can be used to identify and evaluate small molecule that modulate ion and protein transport.

When 108P5H8 functions as an ion channel, it is used as a target for diagnostic, preventative and therapeutic purposes.

Example 50 Detection of 108P5H8 Protein in LNCaP Cells, a Prostate Cancer Cell Line by Immunocytochemistry

To assess the expression of 108P5H8 protein in a prostate cancer cell line, preparations of cytocentrifuged LNCaP cells were stained using a rabbit polyclonal antibody to 108P5H8. Preparations of LNCaP cells were made from three differently treated cell populations to assess whether 108P5H8 is androgen regulated. The LNCaP cell preparations were made from cells grown in medium containing 10% fetal bovine serum; from cells grown for 72 hours in androgen free, serum depleted medium (by growing in charcoal dextran stripped medium); or from previously androgen starved cells which were subsequently stimulated with 10 mmol mibolerone (a synthetic androgen) for 48 hours. The cells were spun down, washed twice (in buffer), resuspended (in buffer) and then centrifuged onto slides (1000 rpm for 2 minutes), allowed to dry and then fixed in acetone for 10 minutes. The cells were then incubated with rabbit polyclonal 108P5H8 for 3 hours (FIG. 26A-C), or rabbit IgG (FIG. 26D). The slides were washed three times in buffer then incubated in DAKO EnVision⁺™ peroxidase conjugated goat anti-rabbit secondary antibody (DAKO Corporation, Carpenteria, Calif.) for 1 hour. The cells were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed strong expression of 108P5H8 in all three LNCaP cell preparations demonstrating that expression of 108P5H8 can be detected in this prostate cancer cell line and is not androgen related. This indicates that antibodies to 108P5H8 are useful in detecting non-androgen related cancer of the prostate; the protein is a useful marker.

Example 51 Detection of 108P5H8 Protein in Prostate Cancer Patient Specimens by Immunohistochemisttry

To assess the expression of 108P5H8 protein, prostate cancer specimens were obtained from prostate cancer patients and stained using a rabbit polyclonal antibody to 108P5H8. Frozen tissues were then cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with rabbit polyclonal 108P5H8 for 3 hours (FIG. 27A), or rabbit IgG (FIG. 27B). The slides were washed three times in buffer then incubated in DAKO EnVision⁺™ peroxidase conjugated goat anti-rabbit secondary antibody (DAKO Corporation, Carpenteria, Calif.) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed strong expression in the neoplastic glands of the prostate (FIG. 27A). These results further confirm the utility of 108P5H8 as a prostate tumor marker.

Throughout this application, various website data content, publications, patent applications and patents are referenced. (Websites are referenced by their Uniform Resource Locator, or URL, addresses on the World Wide Web.) The disclosures of each of these references are hereby incorporated by reference herein in their entireties.

The present invention is not to be limited in scope by the embodiments disclosed herein, which are intended as single illustrations of individual aspects of the invention, and any that are functionally equivalent are within the scope of the invention. Various modifications to the models and methods of the invention, in addition to those described herein, will become apparent to those skilled in the art from the foregoing description and teachings, and are similarly intended to fall within the scope of the invention. Such modifications or other embodiments can be practiced without departing from the true scope and spirit of the invention.

Table

Table I: Tissues that Express 108P5H8 When Malignant

-   -   Prostate     -   Bladder     -   Kidney     -   Colon     -   Lung     -   Ovary     -   Breast     -   Pancreas     -   Uterus     -   Stomach

TABLE II AMINO ACID ABBREVIATIONS SINGLE LETTER THREE LETTER FULL NAME F Phe phenylalanine L Leu leucine S Ser serine Y Tyr tyrosine C Cys cysteine W Trp tryptophan P Pro proline H His histidine Q Gln glutamine R Arg arginine I Ile isoleucine M Met methionine T Thr threonine N Asn asparagine K Lys lysine V Val valine A Ala alanine D Asp aspartic acid E Glu glutamic acid G Gly glycine

TABLE III AMINO ACID SUBSTITUTION MATRIX Adapted from the GCG Software 9.0 BLOSUM62 amino acid substitution matrix (block substitution matrix). The higher the value, the more likely a substitution is found in related, natural proteins. A C D E F G H I K L M N P Q R S T V W Y . 4 0 -2 -1 -2 0 -2 -1 -1 -1 -1 -2 -1 -1 -1 1 0 0 -3 -2 A 9 3 -4 -2 -3 -3 -1 -3 -1 -1 -3 -3 -3 -3 -1 -1 -1 -2 -2 C 6 2 -3 -1 -1 -3 -1 -4 -3 1 -1 0 -2 0 -1 -3 -4 -3 D 5 -3 -2 0 -3 1 -3 -2 0 -1 2 0 0 -1 -2 -3 -2 E 6 -3 -1 0 -3 0 0 -3 -4 -3 -3 -2 -2 -1 1 3 F 6 -2 -4 -2 -4 -3 0 -2 -2 -2 0 -2 -3 -2 -3 G 8 -3 -1 -3 -2 1 -2 0 0 -1 -2 -3 -2 2 H 4 -3 2 1 -3 -3 -3 -3 -2 -1 3 -3 -1 I 5 -2 -1 0 -1 1 2 0 -1 -2 -3 -2 K 4 2 -3 -3 -2 -2 -2 -1 1 -2 -1 L 5 -2 -2 0 -1 -1 -1 1 -1 -1 M 6 -2 0 0 1 0 -3 -4 -2 N 7 -1 -2 -1 -1 -2 -4 -3 P 5 1 0 -1 -2 -2 -1 Q 5 -1 -1 -3 -3 -2 R 4 1 -2 -3 -2 S 5 0 -2 -2 T 4 -3 -1 V 11 2 W 7 Y

TABLE IV (A) POSITION POSITION POSITION 3 (Primary C Terminus 2 (Primary Anchor) Anchor) (Primary Anchor) SUPERMOTIFS A1 TI LVMS FWY A2 LIVM ATQ IV MATL A3 VSMA TLI RK A24 YF WIVLMT FI YWLM B7 P VILF MWYA B27 RHK FYL WMIVA B44 E D FWYLIMVA B58 ATS FWY LIVMA B62 QL IVMP FWYMIVLA MOTIFS A1 TSM Y A1 DE AS Y A2.1 LM VQIAT V LIMAT A3 LMVISATF CGD KYR HFA A11 VTMLISAGN CDF K RYH A24 YFWM FLIW A*3101 MVT ALIS R K A*3301 MVALF IST RK A*6801 AVT MSLI RK B*0702 P LMF WYAIV B*3501 P LMFWY IVA B51 P LIVF WYAM B*5301 P IMFWY ALV B*5401 P ATIV LMFWY Bolded residues are preferred, italicized residues are less preferred: A peptide is considered motif-bearing if it has primary anchors at each primary anchor position for a motif or supermotif as specified in the above table.

TABLE IV (B) HLA CLASS II SUPERMOTIF 1 6 9 W, F, Y, V, I, L A, V, I, L, P, C, S, T A, V, I, L, C, S, T, M, Y

TABLE IV (C) MOTIFS 1° anchor 1 2 3 4 5 1° anchor 6 7 8 9 DR4 preferred FMYLIVW M T I VSTCPALIM MH MH deleterious W R WDE DR1 preferred MFLIVWY PAMQ VMATSPLIC M AVM deleterious C CH FD CWD GDE D DR7 preferred MFLIVWY M W A IVMSACTPL M IV deleterious C G GRD N G DR3 MOTIFS 1° anchor 1 2 3 1° anchor 4 5 1° anchor 6 motif a LIVMFY D preferred motif b LIVMFAY DNQEST KRH preferred DR MFLIVWY VMSTACPLI Super- motif Italicized residues indicate less preferred or “tolerated” residues.

TABLE V (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - A1, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE ID# 1 23 LNDTSAFDF 6.250 1. 2 148 LTDLSAIIL 6.250 2. 3 141 MTDALHMLT 6.250 3. 4 303 IADPICTYV 5.000 4. 5 94 SCDNCSKQR 5.000 5. 6 356 SVEDLNIWS 4.500 6. 7 192 YILMGFLLY 2.500 7. 8 377 QLIPGSSSK 2.000 8. 9 178 RLEVLSAMI 1.800 9. 10 54 GSEAPERPV 1.350 10. 11 184 AMISVLLVY 1.250 11. 12 35 AGDEGLSRF 1.250 12. 13 285 SVGVLIAAY 1.000 13. 14 113 RLTIAAVLY 1.000 14. 15 76 LLDQDLPLT 1.000 15. 16 101 QREILKQRK 0.900 16. 17 331 ILEGVPSHL 0.900 17. 18 166 KSPTKRFTF 0.750 18. 19 31 FSDEAGDEG 0.750 19. 20 214 NGDIMLITA 0.625 20. 21 91 KVDSCDNCS 0.500 21. 22 34 EAGDEGLSR 0.500 22. 23 116 IAAVLYLLF 0.500 23. 24 288 VLIAAYIIR 0.500 24. 25 405 RCTIQLQSY 0.500 25. 26 340 NVDYIKEAL 0.500 26. 27 226 VAVNVIMGF 0.500 27. 28 289 LIAAYIIRF 0.500 28. 29 396 LLLNTFGMY 0.500 29. 30 125 MIGELVGGY 0.500 30. 31 397 LLNTFGMYR 0.500 31. 32 302 KIADPICTY 0.500 32. 33 83 LTNSQLSLK 0.500 33. 34 189 LLVYILMGF 0.500 34. 35 162 WLSSKSPTK 0.400 35. 36 267 DSLAVRAAF 0.300 36. 37 3 GSGAWKRLK 0.300 37. 38 70 QADDDSLLD 0.250 38. 39 406 CTIQLQSYR 0.250 39. 40 335 VPSHLNVDY 0.250 40. 41 126 IGELVGGYI 0.225 41. 42 290 IAAYIIRFK 0.200 42. 43 310 YVFSLLVAF 0.200 43. 44 248 SLPSNSPTR 0.200 44. 45 197 FLLYEAVQR 0.200 45. 46 158 LLALWLSSK 0.200 46. 47 98 CSKQREILK 0.150 47. 48 265 GQDSLAVRA 0.150 48. 49 247 HSLPSNSPT 0.150 49. 50 414 RQEVDRTCA 0.135 50.

TABLE VI (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - A1, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE ID# 1 303 IADPICTYVF 100.000 51. 2 91 KVDSCDNCSK 10.000 52. 3 148 LTDLSAIILT 6.250 53. 4 36 GDEGLSRFNK 4.500 54. 5 178 RLEVLSAMIS 4.500 55. 6 247 HSLPSNSPTR 3.000 56. 7 54 GSEAPERPVN 2.700 57. 8 76 LLDQDLPLTN 2.500 58. 9 183 SAMISVLLVY 2.500 59. 10 70 QADDDSLLDQ 2.500 60. 11 284 QSVGVLIAAY 1.500 61. 12 340 NVDYIKEALM 1.000 62. 13 334 GVPSHLNVDY 1.000 63. 14 356 SVEDLNIWSL 0.900 64. 15 331 ILEGVPSHLN 0.900 65. 16 31 FSDEAGDEGL 0.750 66. 17 141 MTDALHMLTD 0.625 67. 18 396 LLLNTFGMYR 0.500 68. 19 225 GVAVNVIMGF 0.500 69. 20 22 FLNDTSAFDF 0.500 70. 21 287 GVLIAAYIIR 0.500 71. 22 346 EALMKIEDVY 0.500 72. 23 51 ADDGSEAPER 0.500 73. 24 188 VLLVYILMGF 0.500 74. 25 395 HLLLNTFGMY 0.500 75. 26 288 VLIAAYIIRF 0.500 76. 27 115 TIAAVLYLLF 0.500 77. 28 126 IGELVGGYIA 0.450 78. 29 165 SKSPTKRFTF 0.250 79. 30 202 AVQRTIHMNY 0.250 80. 31 124 FMIGELVGGY 0.250 81. 32 279 LGDLVQSVGV 0.250 82. 33 298 KPEYKIADPI 0.225 83. 34 210 NYEINGDIML 0.225 84. 35 157 TLLALWLSSK 0.200 85. 36 289 LIAAYIIRFK 0.200 86. 37 350 KIEDVYSVED 0.180 87. 38 93 DSCDNCSKQR 0.150 88. 39 312 FSLLVAFTTF 0.150 89. 40 414 RQEVDRTCAN 0.135 90. 41 15 RKDDAPLFLN 0.125 91. 42 156 LTLLALWLSS 0.125 92. 43 83 LTNSQLSLKV 0.125 93. 44 172 FTFGFHRLEV 0.125 94. 45 214 NGDIMLITAA 0.125 95. 46 308 CTYVFSLLVA 0.125 96. 47 23 LNDTSAFDFS 0.125 97. 48 35 AGDEGLSRFN 0.125 98. 49 191 VYILMGFLLY 0.125 99. 50 97 NCSKQREILK 0.100 100.

TABLE VII (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - A2, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE ID# 1 278 ALGDLVQSV 655.875 101. 2 268 SLAVRAAFV 382.536 102. 3 198 LLYEAVQRT 382.282 103. 4 75 SLLDQDLPL 324.068 104. 5 140 IMTDALHML 247.333 105. 6 122 LLFMIGELV 214.366 106. 7 155 ILTLLALWL 199.738 107. 8 218 MLITAAVGV 118.238 108. 9 121 YLLFMIGEL 108.713 109. 10 323 IIWDTVVII 78.258 110. 11 409 QLQSYRQEV 69.552 111. 12 402 GMYRCTIQL 49.371 112. 13 118 AVLYLLFMI 45.057 113. 14 181 VLSAMISVL 34.246 114. 15 185 MISVLLVYI 30.849 115. 16 147 MLTDLSAII 29.814 116. 17 190 LVYILMGFL 16.722 117. 18 69 LQADDDSLL 15.096 118. 19 194 LMGFLLYEA 14.029 119. 20 275 FVHALGDLV 13.717 120. 21 308 CTYVFSLLV 11.747 121. 22 76 LLDQDLPLT 11.655 122. 23 137 SLAIMTDAL 10.468 123. 24 68 TLQADDDSL 10.468 124. 25 315 LVAFTTFRI 9.001 125. 26 183 SAMISVLLV 8.221 126. 27 327 TVVIILEGV 6.859 127. 28 115 TIAAVLYLL 6.756 128. 29 153 AIILTLLAL 6.756 129. 30 319 TTFRIIWDT 6.606 130. 31 114 LTIAAVLYL 6.381 131. 32 87 QLSLKVDSC 5.599 132. 33 364 SLTSGKSTA 4.968 133. 34 357 VEDLNIWSL 4.872 134. 35 312 FSLLVAFTT 4.802 135. 36 193 ILMGFLLYE 4.506 136. 37 180 EVLSAMISV 3.884 137. 38 150 DLSAIILTL 3.685 138. 39 389 VQSKANHLL 3.682 139. 40 395 HLLLNTFGM 3.625 140. 41 303 IADPICTYV 3.613 141. 42 227 AVNVIMGFL 3.074 142. 43 49 VVADDGSEA 3.030 143. 44 133 YIANSLAIM 2.963 144. 45 13 MLRKDDAPL 2.760 145. 46 216 DIMLITAAV 2.654 146. 47 139 AIMTDALHM 2.527 147. 48 187 SVLLVYILM 2.413 148. 49 331 ILEGVPSHL 2.324 149. 50 146 HMLTDLSAI 2.180 150.

TABLE VIII (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - A2, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE ID# 1 302 KIADPICTYV 754.791 151. 2 121 YLLFMIGELV 580.050 152. 3 217 IMLITAAVGV 315.959 153. 4 197 FLLYEAVQRT 291.716 154. 5 113 RLTIAAVLYL 270.234 155. 6 75 SLLDQDLPLT 260.008 156. 7 323 IIWDTVVIIL 160.242 157. 8 310 YVFSLLVAFT 140.388 158. 9 314 LLVAFTTFRI 102.867 159. 10 154 IILTLLALWL 101.617 160. 11 184 AMISVLLVYI 95.315 161. 12 330 IILEGVPSHL 75.751 162. 13 193 ILMGFLLYEA 71.872 163. 14 39 GLSRFNKLRV 69.552 164. 15 194 LMGFLLYEAV 62.765 165. 16 160 ALWLSSKSPT 61.852 166. 17 147 MLTDLSAIIL 61.047 167. 18 189 LLVYILMGFL 59.722 168. 19 190 LVYILMGFLL 58.977 169. 20 12 SMLRKDDAPL 57.085 170. 21 198 LLYEAVQRTI 46.539 171. 22 408 IQLQSYRQEV 44.356 172. 23 140 IMTDALHMLT 37.513 173. 24 181 VLSAMISVLL 36.316 174. 25 139 AIMTDALHML 24.997 175. 26 68 TLQADDDSLL 21.362 176. 27 397 LLNTFGMYRC 19.425 177. 28 172 FTFGFHRLEV 16.441 178. 29 219 LITAAVGVAV 16.258 179. 30 227 AVNVIMGFLL 10.841 180. 31 364 SLTSGKSTAI 10.433 181. 32 356 SVEDLNIWSL 8.461 182. 33 318 FTTFRIIWDT 8.213 183. 34 22 FLNDTSAFDF 8.152 184. 35 125 MIGELVGGYI 7.149 185. 36 348 LMKIEDVYSV 6.874 186. 37 345 KEALMKIEDV 5.335 187. 38 179 LEVLSAMISV 5.288 188. 39 285 SVGVLIAAYI 5.021 189. 40 144 ALHMLTDLSA 4.968 190. 41 133 YIANSLAIMT 4.713 191. 42 185 MISVLLVYIL 4.709 192. 43 150 DLSAIILTLL 3.685 193. 44 389 VQSKANHLLL 3.682 194. 45 129 LVGGYIANSL 3.178 195. 46 319 TTFRIIWDTV 2.977 196. 47 307 ICTYVFSLLV 2.933 197. 48 5 GAWKRLKSML 2.463 198. 49 401 FGMYRCTIQL 2.373 199. 50 332 LEGVPSHLNV 2.299 200.

TABLE IX (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - A3, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE ID# 1 158 LLALWLSSK 90.000 201. 2 377 QLIPGSSSK 45.000 202. 3 184 AMISVLLVY 27.000 203. 4 397 LLNTFGMYR 24.000 204. 5 162 WLSSKSPTK 20.000 205. 6 39 GLSRFNKLR 18.000 206. 7 402 GMYRCTIQL 18.000 207. 8 314 LLVAFTTFR 18.000 208. 9 189 LLVYILMGF 13.500 209. 10 288 VLIAAYIIR 12.000 210. 11 361 NIWSLTSGK 10.000 211. 12 347 ALMKIEDVY 9.000 212. 13 313 SLLVAFTTF 9.000 213. 14 197 FLLYEAVQR 6.000 214. 15 396 LLLNTFGMY 5.400 215. 16 113 RLTIAAVLY 4.000 216. 17 248 SLPSNSPTR 4.000 217. 18 192 YILMGFLLY 3.600 218. 19 302 KIADPICTY 2.700 219. 20 198 LLYEAVQRT 2.250 220. 21 294 IIRFKPEYK 2.000 221. 22 289 LIAAYIIRF 1.800 222. 23 293 YIIRFKPEY 1.800 223. 24 234 FLLNQSGHR 1.800 224. 25 75 SLLDQDLPL 1.800 225. 26 122 LLFMIGELV 1.500 226. 27 310 YVFSLLVAF 1.500 227. 28 83 LTNSQLSLK 1.500 228. 29 146 HMLTDLSAI 1.350 229. 30 331 ILEGVPSHL 1.350 230. 31 155 ILTLLALWL 1.200 231. 32 181 VLSAMISVL 0.900 232. 33 395 HLLLNTFGM 0.900 233. 34 194 LMGFLLYEA 0.900 234. 35 323 IIWDTVVII 0.900 235. 36 140 IMTDALHML 0.900 236. 37 150 DLSAIILTL 0.810 237. 38 287 GVLIAAYII 0.810 238. 39 100 KQREILKQR 0.608 239. 40 278 ALGDLVQSV 0.600 240. 41 409 QLQSYRQEV 0.600 241. 42 137 SLAIMTDAL 0.600 242. 43 68 TLQADDDSL 0.600 243. 44 285 SVGVLIAAY 0.600 244. 45 178 RLEVLSAMI 0.600 245. 46 119 VLYLLFMIG 0.600 246. 47 147 MLTDLSAII 0.600 247. 48 13 MLRKDDAPL 0.600 248. 49 87 QLSLKVDSC 0.600 249. 50 170 KRFTFGFHR 0.540 250.

TABLE X (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - A3, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE ID# 1 157 TLLALWLSSK 135.000 251. 2 396 LLLNTFGMYR 36.000 252. 3 288 VLIAAYIIRF 27.000 253. 4 313 SLLVAFTTFR 18.000 254. 5 188 VLLVYILMGF 13.500 255. 6 124 FMIGELVGGY 8.100 256. 7 22 FLNDTSAFDF 6.000 257. 8 91 KVDSCDNCSK 6.000 258. 9 104 ILKQRKVKAR 6.000 259. 10 395 HLLLNTFGMY 5.400 260. 11 162 WLSSKSPTKR 4.000 261. 12 287 GVLIAAYIIR 3.600 262. 13 113 RLTIAAVLYL 3.600 263. 14 293 YIIRFKPEYK 3.000 264. 15 82 PLTNSQLSLK 3.000 265. 16 100 KQREILKQRK 2.700 266. 17 323 IIWDTVVIIL 2.700 267. 18 314 LLVAFTTFRI 2.700 268. 19 225 GVAVNVIMGF 2.700 269. 20 193 ILMGFLLYEA 2.025 270. 21 13 MLRKDDAPLF 2.000 271. 22 348 LMKIEDVYSV 1.800 272. 23 184 AMISVLLVYI 1.350 273. 24 334 GVPSHLNVDY 1.200 274. 25 147 MLTDLSAIIL 1.200 275. 26 39 GLSRFNKLRV 1.200 276. 27 202 AVQRTIHMNY 1.200 277. 28 20 PLFLNDTSAF 1.000 278. 29 376 IQLIPGSSSK 0.900 279. 30 190 LVYILMGFLL 0.900 280. 31 181 VLSAMISVLL 0.900 281. 32 12 SMLRKDDAPL 0.900 282. 33 119 VLYLLFMIGE 0.900 283. 34 397 LLNTFGMYRC 0.900 284. 35 146 HMLTDLSAII 0.900 285. 36 198 LLYEAVQRTI 0.675 286. 37 399 NTFGMYRCTI 0.675 287. 38 68 TLQADDDSLL 0.600 288. 39 364 SLTSGKSTAI 0.600 289. 40 268 SLAVRAAFVH 0.600 290. 41 270 AVRAAFVHAL 0.540 291. 42 185 MISVLLVYIL 0.540 292. 43 160 ALWLSSKSPT 0.500 293. 44 402 GMYRCTIQLQ 0.450 294. 45 289 LIAAYIIRFK 0.450 295. 46 338 HLNVDYIKEA 0.450 296. 47 121 YLLFMIGELV 0.450 297. 48 197 FLLYEAVQRT 0.450 298. 49 377 QLIPGSSSKW 0.450 299. 50 150 DLSAIILTLL 0.405 300.

TABLE XI (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - A11, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE ID# 1 83 LTNSQLSLK 1.000 301. 2 361 NIWSLTSGK 0.800 302. 3 377 QLIPGSSSK 0.600 303. 4 294 IIRFKPEYK 0.400 304. 5 162 WLSSKSPTK 0.400 305. 6 158 LLALWLSSK 0.400 306. 7 342 DYIKEALMK 0.360 307. 8 406 CTIQLQSYR 0.300 308. 9 288 VLIAAYIIR 0.240 309. 10 8 KRLKSMLRK 0.180 310. 11 287 GVLIAAYII 0.180 311. 12 100 KQREILKQR 0.180 312. 13 397 LLNTFGMYR 0.160 313. 14 39 GLSRFNKLR 0.120 314. 15 197 FLLYEAVQR 0.120 315. 16 234 FLLNQSGHR 0.120 316. 17 314 LLVAFTTFR 0.120 317. 18 205 RTIHMNYEI 0.090 318. 19 118 AVLYLLFMI 0.090 319. 20 103 EILKQRKVK 0.090 320. 21 248 SLPSNSPTR 0.080 321. 22 1 MAGSGAWKR 0.080 322. 23 170 KRFTFGFHR 0.072 323. 24 337 SHLNVDYIK 0.060 324. 25 315 LVAFTTFRI 0.060 325. 26 109 KVKARLTIA 0.060 326. 27 187 SVLLVYILM 0.060 327. 28 37 DEGLSRFNK 0.054 328. 29 402 GMYRCTIQL 0.048 329. 30 190 LVYILMGFL 0.040 330. 31 310 YVFSLLVAF 0.040 331. 32 308 CTYVFSLLV 0.040 332. 33 384 SKWEEVQSK 0.040 333. 34 98 CSKQREILK 0.040 334. 35 132 GYIANSLAI 0.036 335. 36 327 TVVIILEGV 0.030 336. 37 114 LTIAAVLYL 0.030 337. 38 34 EAGDEGLSR 0.024 338. 39 275 FVHALGDLV 0.020 339. 40 94 SCDNCSKQR 0.020 340. 41 49 VVADDGSEA 0.020 341. 42 282 LVQSVGVLI 0.020 342. 43 290 IAAYIIRFK 0.020 343. 44 223 AVGVAVNVI 0.020 344. 45 92 VDSCDNCSK 0.020 345. 46 285 SVGVLIAAY 0.020 346. 47 340 NVDYIKEAL 0.020 347. 48 227 AVNVIMGFL 0.020 348. 49 270 AVRAAFVHA 0.020 349. 50 101 QREILKQRK 0.020 350.

TABLE XII (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - A11, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID# 1 91 KVDSCDNCSK 6.000 351. 2 287 GVLIAAYIIR 3.600 352. 3 100 KQREILKQRK 1.800 353. 4 376 IQLIPGSSSK 0.900 354. 5 157 TLLALWLSSK 0.600 355. 6 293 YIIRFKPEYK 0.600 356. 7 97 NCSKQREILK 0.400 357. 8 396 LLLNTFGMYR 0.240 358. 9 36 GDEGLSRFNK 0.180 359. 10 196 GFLLYEAVQR 0.180 360. 11 233 GFLLNQSGHR 0.180 361. 12 102 REILKQRKVK 0.135 362. 13 225 GVAVNVIMGF 0.120 363. 14 190 LVYILMGFLL 0.120 364. 15 109 KVKARLTIAA 0.120 365. 16 410 LQSYRQEVDR 0.120 366. 17 405 RCTIQLQSYR 0.120 367. 18 313 SLLVAFTTFR 0.120 368. 19 162 WLSSKSPTKR 0.080 369. 20 341 VDYIKEALMK 0.080 370. 21 360 LNIWSLTSGK 0.060 371. 22 334 GVPSHLNVDY 0.060 372. 23 227 AVNVIMGFLL 0.060 373. 24 253 SPTRGSGCER 0.040 374. 25 7 WKRLKSMLRK 0.040 375. 26 104 ILKQRKVKAR 0.040 376. 27 308 CTYVFSLLVA 0.040 377. 28 282 LVQSVGVLIA 0.040 378. 29 289 LIAAYIIRFK 0.040 379. 30 172 FTFGFHRLEV 0.040 380. 31 356 SVEDLNIWSL 0.040 381. 32 82 PLTNSQLSLK 0.040 382. 33 202 AVQRTIHMNY 0.040 383. 34 161 LWLSSKSPTK 0.030 384. 35 48 VVVADDGSEA 0.030 385. 36 114 LTIAAVLYLL 0.030 386. 37 353 DVYSVEDLNI 0.024 387. 38 39 GLSRFNKLRV 0.024 388. 39 113 RLTIAAVLYL 0.024 389. 40 319 TTFRIIWDTV 0.020 390. 41 223 AVGVAVNVIM 0.020 391. 42 383 SSKWEEVQSK 0.020 392. 43 270 AVRAAFVHAL 0.020 393. 44 399 NTFGMYRCTI 0.020 394. 45 83 LTNSQLSLKV 0.020 395. 46 285 SVGVLIAAYI 0.020 396. 47 129 LVGGYIANSL 0.020 397. 48 340 NVDYIKEALM 0.020 398. 49 314 LLVAFTTFRI 0.018 399. 50 322 RIIWDTVVII 0.018 400.

TABLE XIII (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - A24, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID# 1 191 VYILMGFLL 300.000 401. 2 199 LYEAVQRTI 105.000 402. 3 132 GYIANSLAI 75.000 403. 4 354 VYSVEDLNI 50.000 404. 5 171 RFTFGFHRL 48.000 405. 6 210 NYEINGDIM 37.500 406. 7 274 AFVHALGDL 30.000 407. 8 21 LFLNDTSAF 15.000 408. 9 106 KQRKVKARL 11.200 409. 10 38 EGLSRFNKL 9.504 410. 11 331 ILEGVPSHL 8.400 411. 12 227 AVNVIMGFL 8.400 412. 13 309 TYVFSLLVA 7.500 413. 14 75 SLLDQDLPL 7.200 414. 15 186 ISVLLVYIL 7.200 415. 16 388 EVQSKANHL 7.200 416. 17 130 VGGYIANSL 6.720 417. 18 307 ICTYVFSLL 6.720 418. 19 121 YLLFMIGEL 6.600 419. 20 153 AIILTLLAL 6.000 420. 21 166 KSPTKRFTF 6.000 421. 22 281 DLVQSVGVL 6.000 422. 23 68 TLQADDDSL 6.000 423. 24 143 DALHMLTDL 6.000 424. 25 228 VNVIMGFLL 6.000 425. 26 80 DLPLTNSQL 6.000 426. 27 114 LTIAAVLYL 6.000 427. 28 150 DLSAIILTL 5.600 428. 29 340 NVDYIKEAL 5.600 429. 30 324 IWDTVVIIL 5.600 430. 31 115 TIAAVLYLL 5.600 431. 32 370 STAIVHIQL 5.600 432. 33 151 LSAIILTLL 5.600 433. 34 182 LSAMISVLL 5.600 434. 35 300 EYKIADPIC 5.000 435. 36 400 TFGMYRCTI 5.000 436. 37 412 SYRQEVDRT 5.000 437. 38 6 AWKRLKSML 4.800 438. 39 190 LVYILMGFL 4.800 439. 40 69 LQADDDSLL 4.800 440. 41 155 ILTLLALWL 4.800 441. 42 140 IMTDALHML 4.800 442. 43 189 LLVYILMGF 4.200 443. 44 226 VAVNVIMGF 4.200 444. 45 267 DSLAVRAAF 4.200 445. 46 13 MLRKDDAPL 4.000 446. 47 402 GMYRCTIQL 4.000 447. 48 2 AGSGAWKRL 4.000 448. 49 97 NCSKQREIL 4.000 449. 50 390 QSKANHLLL 4.000 450.

TABLE XIV (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - A24, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID# 1 120 LYLLFMIGEL 330.000 451. 2 210 NYEINGDIML 300.000 452. 3 309 TYVFSLLVAF 180.000 453. 4 342 DYIKEALMKI 82.500 454. 5 132 GYIANSLAIM 37.500 455. 6 173 TFGFHRLEVL 20.000 456. 7 60 RPVNGAHPTL 12.000 457. 8 369 KSTAIVHIQL 11.200 458. 9 111 KARLTIAAVL 11.200 459. 10 339 LNVDYIKEAL 10.080 460. 11 330 IILEGVPSHL 10.080 461. 12 191 VYILMGFLLY 9.000 462. 13 392 KANHLLLNTF 8.640 463. 14 226 VAVNVIMGFL 8.400 464. 15 114 LTIAAVLYLL 8.400 465. 16 292 AYIIRFKPEY 8.250 466. 17 113 RLTIAAVLYL 8.000 467. 18 189 LLVYILMGFL 7.200 468. 19 356 SVEDLNIWSL 7.200 469. 20 154 IILTLLALWL 7.200 470. 21 403 MYRCTIQLQS 7.000 471. 22 412 SYRQEVDRTC 7.000 472. 23 129 LVGGYIANSL 6.720 473. 24 323 IIWDTVVIIL 6.720 474. 25 305 DPICTYVFSL 6.000 475. 26 152 SAIILTLLAL 6.000 476. 27 401 FGMYRCTIQL 6.000 477. 28 12 SMLRKDDAPL 6.000 478. 29 68 TLQADDDSLL 6.000 479. 30 354 VYSVEDLNIW 6.000 480. 31 81 LPLTNSQLSL 6.000 481. 32 227 AVNVIMGFLL 6.000 482. 33 139 AIMTDALHML 6.000 483. 34 136 NSLAIMTDAL 6.000 484. 35 388 EVQSKANHLL 6.000 485. 36 180 EVLSAMISVL 6.000 486. 37 74 DSLLDQDLPL 6.000 487. 38 150 DLSAIILTLL 5.600 488. 39 181 VLSAMISVLL 5.600 489. 40 300 EYKIADPICT 5.000 490. 41 185 MISVLLVYIL 4.800 491. 42 5 GAWKRLKSML 4.800 492. 43 147 MLTDLSAIIL 4.800 493. 44 31 FSDEAGDEGL 4.800 494. 45 298 KPEYKIADPI 4.200 495. 46 188 VLLVYILMGF 4.200 496. 47 273 AAFVHALGDL 4.000 497. 48 270 AVRAAFVHAL 4.000 498. 49 1 MAGSGAWKRL 4.000 499. 50 96 DNCSKQREIL 4.000 500.

TABLE XV (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - B7, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID# 1 227 AVNVIMGFL 60.000 501. 2 106 KQRKVKARL 40.000 502. 3 13 MLRKDDAPL 40.000 503. 4 190 LVYILMGFL 20.000 504. 5 388 EVQSKANHL 20.000 505. 6 270 AVRAAFVHA 15.000 506. 7 2 AGSGAWKRL 12.000 507. 8 143 DALHMLTDL 12.000 508. 9 153 AIILTLLAL 12.000 509. 10 139 AIMTDALHM 9.000 510. 11 117 AAVLYLLFM 9.000 511. 12 340 NVDYIKEAL 6.000 512. 13 97 NCSKQREIL 6.000 513. 14 111 KARLTIAAV 6.000 514. 15 118 AVLYLLFMI 6.000 515. 16 223 AVGVAVNVI 6.000 516. 17 187 SVLLVYILM 5.000 517. 18 150 DLSAIILTL 4.000 518. 19 307 ICTYVFSLL 4.000 519. 20 186 ISVLLVYIL 4.000 520. 21 130 VGGYIANSL 4.000 521. 22 151 LSAIILTLL 4.000 522. 23 182 LSAMISVLL 4.000 523. 24 390 QSKANHLLL 4.000 524. 25 155 ILTLLALWL 4.000 525. 26 402 GMYRCTIQL 4.000 526. 27 75 SLLDQDLPL 4.000 527. 28 69 LQADDDSLL 4.000 528. 29 181 VLSAMISVL 4.000 529. 30 370 STAIVHIQL 4.000 530. 31 114 LTIAAVLYL 4.000 531. 32 281 DLVQSVGVL 4.000 532. 33 80 DLPLTNSQL 4.000 533. 34 389 VQSKANHLL 4.000 534. 35 38 EGLSRFNKL 4.000 535. 36 115 TIAAVLYLL 4.000 536. 37 140 IMTDALHML 4.000 537. 38 68 TLQADDDSL 4.000 538. 39 174 FGFHRLEVL 4.000 539. 40 228 VNVIMGFLL 4.000 540. 41 121 YLLFMIGEL 4.000 541. 42 137 SLAIMTDAL 4.000 542. 43 5 GAWKRLKSM 3.000 543. 44 201 EAVQRTIHM 3.000 544. 45 57 APERPVNGA 2.700 545. 46 61 PVNGAHPTL 2.000 546. 47 282 LVQSVGVLI 2.000 547. 48 287 GVLIAAYII 2.000 548. 49 315 LVAFTTFRI 2.000 549. 50 40 LSRFNKLRV 2.000 550.

TABLE XVI (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - B7, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID# 1 270 AVRAAFVHAL 600.000 551. 2 111 KARLTIAAVL 120.000 552. 3 60 RPVNGAHPTL 80.000 553. 4 81 LPLTNSQLSL 80.000 554. 5 305 DPICTYVFSL 80.000 555. 6 227 AVNVIMGFLL 60.000 556. 7 273 AAFVHALGDL 36.000 557. 8 139 AIMTDALHML 36.000 558. 9 388 EVQSKANHLL 20.000 559. 10 180 EVLSAMISVL 20.000 560. 11 190 LVYILMGFLL 20.000 561. 12 129 LVGGYIANSL 20.000 562. 13 223 AVGVAVNVIM 15.000 563. 14 5 GAWKRLKSML 12.000 564. 15 1 MAGSGAWKRL 12.000 565. 16 152 SAIILTLLAL 12.000 566. 17 401 FGMYRCTIQL 12.000 567. 18 226 VAVNVIMGFL 12.000 568. 19 335 VPSHLNVDYI 8.000 569. 20 356 SVEDLNIWSL 6.000 570. 21 19 APLFLNDTSA 6.000 571. 22 96 DNCSKQREIL 6.000 572. 23 294 IIRFKPEYKI 6.000 573. 24 113 RLTIAAVLYL 4.000 574. 25 150 DLSAIILTLL 4.000 575. 26 339 LNVDYIKEAL 4.000 576. 27 240 GHRHSHSHSL 4.000 577. 28 147 MLTDLSAIIL 4.000 578. 29 330 IILEGVPSHL 4.000 579. 30 114 LTIAAVLYLL 4.000 580. 31 189 LLVYILMGFL 4.000 581. 32 12 SMLRKDDAPL 4.000 582. 33 74 DSLLDQDLPL 4.000 583. 34 185 MISVLLVYIL 4.000 584. 35 260 CERNHGQDSL 4.000 585. 36 181 VLSAMISVLL 4.000 586. 37 323 IIWDTVVIIL 4.000 587. 38 68 TLQADDDSLL 4.000 588. 39 136 NSLAIMTDAL 4.000 589. 40 154 IILTLLALWL 4.000 590. 41 369 KSTAIVHIQL 4.000 591. 42 389 VQSKANHLLL 4.000 592. 43 117 AAVLYLLFMI 3.600 593. 44 222 AAVGVAVNVI 3.600 594. 45 138 LAIMTDALHM 3.000 595. 46 116 IAAVLYLLFM 3.000 596. 47 298 KPEYKIADPI 2.400 597. 48 315 LVAFTTFRII 2.000 598. 49 285 SVGVLIAAYI 2.000 599. 50 40 LSRFNKLRVV 2.000 600.

TABLE XVII (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - B35, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID# 1 335 VPSHLNVDY 40.000 601. 2 390 QSKANHLLL 15.000 602. 3 164 SSKSPTKRF 15.000 603. 4 166 KSPTKRFTF 10.000 604. 5 302 KIADPICTY 8.000 605. 6 355 YSVEDLNIW 7.500 606. 7 201 EAVQRTIHM 6.000 607. 8 5 GAWKRLKSM 6.000 608. 9 203 VQRTIHMNY 6.000 609. 10 117 AAVLYLLFM 6.000 610. 11 106 KQRKVKARL 6.000 611. 12 267 DSLAVRAAF 5.000 612. 13 151 LSAIILTLL 5.000 613. 14 182 LSAMISVLL 5.000 614. 15 186 ISVLLVYIL 5.000 615. 16 13 MLRKDDAPL 4.500 616. 17 60 RPVNGAHPT 4.000 617. 18 125 MIGELVGGY 4.000 618. 19 113 RLTIAAVLY 4.000 619. 20 405 RCTIQLQSY 4.000 620. 21 111 KARLTIAAV 3.600 621. 22 143 DALHMLTDL 3.000 622. 23 69 LQADDDSLL 3.000 623. 24 116 IAAVLYLLF 3.000 624. 25 40 LSRFNKLRV 3.000 625. 26 226 VAVNVIMGF 3.000 626. 27 139 AIMTDALHM 3.000 627. 28 343 YIKEALMKI 2.400 628. 29 383 SSKWEEVQS 2.250 629. 30 19 APLFLNDTS 2.000 630. 31 192 YILMGFLLY 2.000 631. 32 293 YIIRFKPEY 2.000 632. 33 184 AMISVLLVY 2.000 633. 34 75 SLLDQDLPL 2.000 634. 35 187 SVLLVYILM 2.000 635. 36 224 VGVAVNVIM 2.000 636. 37 81 LPLTNSQLS 2.000 637. 38 133 YIANSLAIM 2.000 638. 39 347 ALMKIEDVY 2.000 639. 40 305 DPICTYVFS 2.000 640. 41 285 SVGVLIAAY 2.000 641. 42 140 IMTDALHML 2.000 642. 43 395 HLLLNTFGM 2.000 643. 44 396 LLLNTFGMY 2.000 644. 45 68 TLQADDDSL 1.500 645. 46 371 TAIVHIQLI 1.200 646. 47 316 VAFTTFRII 1.200 647. 48 322 RIIWDTVVI 1.200 648. 49 97 NCSKQREIL 1.000 649. 50 181 VLSAMISVL 1.000 650.

TABLE XVIII (A) HLA PEPTIDE SCORING RESULTS - 108P5H8 - B35, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID# 1 60 RPVNGAHPTL 40.000 651. 2 305 DPICTYVFSL 20.000 652. 3 81 LPLTNSQLSL 20.000 653. 4 167 SPTKRFTFGF 20.000 654. 5 111 KARLTIAAVL 18.000 655. 6 369 KSTAIVHIQL 10.000 656. 7 284 QSVGVLIAAY 10.000 657. 8 186 ISVLLVYILM 10.000 658. 9 138 LAIMTDALHM 9.000 659. 10 335 VPSHLNVDYI 8.000 660. 11 392 KANHLLLNTF 6.000 661. 12 34 EAGDEGLSRF 6.000 662. 13 346 EALMKIEDVY 6.000 663. 14 116 IAAVLYLLFM 6.000 664. 15 183 SAMISVLLVY 6.000 665. 16 136 NSLAIMTDAL 5.000 666. 17 74 DSLLDQDLPL 5.000 667. 18 312 FSLLVAFTTF 5.000 668. 19 163 LSSKSPTKRF 5.000 669. 20 298 KPEYKIADPI 4.800 670. 21 13 MLRKDDAPLF 4.500 671. 22 209 MNYEINGDIM 4.000 672. 23 40 LSRFNKLRVV 3.000 673. 24 270 AVRAAFVHAL 3.000 674. 25 273 AAFVHALGDL 3.000 675. 26 226 VAVNVIMGFL 3.000 676. 27 5 GAWKRLKSML 3.000 677. 28 1 MAGSGAWKRL 3.000 678. 29 152 SAIILTLLAL 3.000 679. 30 31 FSDEAGDEGL 3.000 680. 31 19 APLFLNDTSA 2.000 681. 32 4 SGAWKRLKSM 2.000 682. 33 113 RLTIAAVLYL 2.000 683. 34 395 HLLLNTFGMY 2.000 684. 35 147 MLTDLSAIIL 2.000 685. 36 334 GVPSHLNVDY 2.000 686. 37 66 HPTLQADDDS 2.000 687. 38 339 LNVDYIKEAL 2.000 688. 39 249 LPSNSPTRGS 2.000 689. 40 323 IIWDTVVIIL 2.000 690. 41 330 IILEGVPSHL 2.000 691. 42 202 AVQRTIHMNY 2.000 692. 43 124 FMIGELVGGY 2.000 693. 44 22 FLNDTSAFDF 2.000 694. 45 223 AVGVAVNVIM 2.000 695. 46 164 SSKSPTKRFT 1.500 696. 47 390 QSKANHLLLN 1.500 697. 48 12 SMLRKDDAPL 1.500 698. 49 68 TLQADDDSLL 1.500 699. 50 316 VAFTTFRIIW 1.500 700.

TABLE V (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - A1, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID# 1 23 LNDTSAFEF 6.250 701. 2 28 AFEFSDEAG 0.045 702. 3 25 DTSAFEFSD 0.013 703. 4 28 SAFEFSDEA 0.010 704. 5 22 FLNDTSAFE 0.002 705. 6 26 TSAFEFSDE 0.002 706. 7 24 NDTSAFEFS 0.001 707. 8 29 FEFSDEAGD 0.000 708. 9 30 EFSDEAGDE 0.000 709.

TABLE VI (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - A1, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID# 1 22 FLNDTSAFEF 0.500 710. 2 23 LNDTSAFEFS 0.125 711. 3 26 TSAFEFSDEA 0.015 712. 4 27 SAFEFSDEAG 0.010 713. 5 28 AFEFSDEAGD 0.009 714. 6 25 DTSAFEFSDE 0.003 715. 7 30 EFSDEAGDEG 0.001 716. 8 24 NDTSAFEFSD 0.000 717. 9 21 LFLNDTSAFE 0.000 718. 10 29 FEFSDEAGDE 0.000 719.

TABLE VII (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - A2, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID# 1 27 SAFEFSDEA 1.949 720. 2 22 FLNDTSAFE 1.546 721. 3 29 FEFSDEAGD 0.005 722. 4 23 LNDTSAFEF 0.002 723. 5 24 NDTSAFEFS 0.001 724. 6 25 DTSAFEFSD 0.000 725. 7 26 TSAFEFSDE 0.000 726. 8 28 AFEFSDEAG 0.000 727. 9 30 EFSDEAGDE 0.000 728.

TABLE VIII (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - A2, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION SUBSEQUENCE OF A MOLECULE START RESIDUE CONTAINING THIS SEQ. RANK POSITION LISTING SEQUENCE) ID # 1 22 FLNDTSAFEF 8.152 729. 2 26 TSAFEFSDEA 0.060 730. 3 27 SAFEFSDEAG 0.008 731. 4 23 LNDTSAFEFS 0.002 732. 5 29 FEFSDEAGDE 0.001 733. 6 24 NDTSAFEFSD 0.000 734. 7 21 LFLNDTSAFE 0.000 735. 8 25 DTSAFEFSDE 0.000 736. 9 30 EFSDEAGDEG 0.000 737. 10 28 AFEFSDEAGD 0.000 738.

TABLE IX (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - A3, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION SUBSEQUENCE OF A MOLECULE START RESIDUE CONTAINING THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID # 1 27 SAFEFSDEA 0.045 739. 2 22 FLNDTSAFE 0.020 740. 3 23 LNDTSAFEF 0.012 741. 4 25 DTSAFEFSD 0.003 742. 5 29 FEFSDEAGD 0.000 743. 6 26 TSAFEFSDE 0.000 744. 7 24 NDTSAFEFS 0.000 745. 8 28 AFEFSDEAG 0.000 746. 9 30 EFSDEAGDE 0.000 747.

TABLE X (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - A3, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION SUBSEQUENCE OF A MOLECULE START RESIDUE CONTAINING THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID # 1 22 FLNDTSAFEF 6.000 748. 2 26 TSAFEFSDEA 0.003 749. 3 27 SAFEFSDEAG 0.002 750. 4 25 DTSAFEFSDE 0.001 751. 5 23 LNDTSAFEFS 0.000 752. 6 24 NDTSAFEFSD 0.000 753. 7 29 FEFSDEAGDE 0.000 754. 8 21 LFLNDTSAFE 0.000 755. 9 28 AFEFSDEAGD 0.000 756. 10 30 EFSDEAGDEG 0.000 757.

TABLE XI (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - All, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION SUBSEQUENCE OF A MOLECULE START RESIDUE CONTAINING THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID # 1 27 SAFEFSDEA 0.004 758. 2 23 LNDTSAFEF 0.001 759. 3 25 DTSAFEFSD 0.001 760. 4 22 FLNDTSAFE 0.000 761. 5 28 AFEFSDEAG 0.000 762. 6 29 FEFSDEAGD 0.000 763. 7 30 EFSDEAGDE 0.000 764. 8 24 NDTSAFEFS 0.000 765. 9 26 TSAFEFSDE 0.000 766.

TABLE XII (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - All, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION SUBSEQUENCE OF A MOLECULE START RESIDUE CONTAINING THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID # 1 22 FLNDTSAFEF 0.012 767. 2 27 SAFEFSDEAG 0.000 768. 3 21 LFLNDTSAFE 0.000 769. 4 25 DTSAFEFSDE 0.000 770. 5 28 AFEFSDEAGD 0.000 771. 6 26 TSAFEFSDEA 0.000 772. 7 29 FEFSDEAGDE 0.000 773. 8 24 NDTSAFEFSD 0.000 774. 9 30 EFSDEAGDEG 0.000 775. 10 23 LNDTSAFEFS 0.000 776.

TABLE XIII (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - A24, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION SUBSEQUENCE OF A MOLECULE START RESIDUE CONTAINING THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID # 1 23 LNDTSAFEF 2.200 777. 2 27 SAFEFSDEA 0.132 778. 3 28 AFEFSDEAG 0.075 779. 4 30 EFSDEAGDE 0.060 780. 5 22 FLNDTSAFE 0.018 781. 6 24 NDTSAFEFS 0.012 782. 7 26 TSAFEFSDE 0.012 783. 8 25 DTSAFEFSD 0.010 784. 9 29 FEFSDEAGD 0.001 785.

TABLE XIV (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - A24, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION SUBSEQUENCE OF A MOLECULE START RESIDUE CONTAINING THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID # 1 22 FLNDTSAFEF 3.960 786. 2 23 LNDTSAFEFS 0.120 787. 3 26 TSAFEFSDEA 0.110 788. 4 28 AFEFSDEAGD 0.075 789. 5 21 LFLNDTSAFE 0.075 790. 6 30 EFSDEAGDEG 0.066 791. 7 27 SAFEFSDEAG 0.012 792. 8 25 DTSAFEFSDE 0.012 793. 9 24 NDTSAFEFSD 0.001 794. 10 29 FEFSDEAGDE 0.001 795.

TABLE XV (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - B7, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION SUBSEQUENCE OF A MOLECULE START RESIDUE CONTAINING THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID # 1 27 SAFEFSDEA 0.300 796. 2 22 FLNDTSAFE 0.010 797. 3 26 TSAFEFSDE 0.010 798. 4 25 DTSAFEFSD 0.010 799. 5 23 LNDTSAFEF 0.006 800. 6 24 NDTSAFEFS 0.002 801. 7 30 EFSDEAGDE 0.001 802. 8 29 FEFSDEAGD 0.001 803. 9 28 AFEFSDEAG 0.001 804.

TABLE XVI (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - B7, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION SUBSEQUENCE OF A MOLECULE START RESIDUE CONTAINING THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID # 1 26 TSAFEFSDEA 0.100 805. 2 27 SAFEFSDEAG 0.030 806. 3 22 FLNDTSAFEF 0.020 807. 4 25 DTSAFEFSDE 0.010 808. 5 23 LNDTSAFEFS 0.006 809. 6 30 EFSDEAGDEG 0.001 810 7 24 NDTSAFEFSD 0.001 811. 8 29 FEFSDEAGDE 0.001 812. 9 21 LFLNDTSAFE 0.001 813. 10 28 AFEFSDEAGD 0.001 814.

TABLE XVII (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - B35, 9-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION SUBSEQUENCE OF A MOLECULE START RESIDUE CONTAINING THIS SEQ. RANK POSITION LISTING SUBSEQUENCE) ID # 1 276 SAFEFSDEA 0.600 815. 2 23 LNDTSAFEF 0.300 816. 3 26 TSAFEFSDE 0.075 817. 4 22 FLNDTSAFE 0.020 818. 5 24 NDTSAFEFS 0.010 819. 6 25 DTSAFEFSD 0.010 820. 7 30 EFSDEAGDE 0.003 821. 8 29 FEFSDEAGD 0.002 822. 9 28 AFEFSDEAG 0.000 823.

TABLE XVIII (B) unique to variant 3 relative to variants 1 and 2 HLA PEPTIDE SCORING RESULTS - 108P5H8 - B35, 10-MERS SCORE (ESTIMATE OF HALF TIME OF DISASSOCIATION OF A MOLECULE SUBSEQUENCE CONTAINING START RESIDUE THIS SEQ. RANK POSITION LISTING SUBSEQUENCE ID# 1 22 FLNDTSAFEF 2.000 824. 2 26 TSAFEFSDEA 0.500 825. 3 27 SAFEFSDEAG 0.060 826. 4 23 LNDTSAFEFS 0.030 827. 5 25 DTSAFEFSDE 0.015 828. 6 30 EFSDEAGDEG 0.002 829. 7 29 FEFSDEAGDE 0.002 830. 8 24 NDTSAFEFSD 0.001 831. 9 21 LFLNDTSAFE 0.001 832. 10 28 AFEFSDEAGD 0.000 833.

TABLE XIX Motifs and Post-translational Modifications of 108P5H8 N-glycosylation site Number of matches: 3 1 24-27 NDTS (SEQ. ID. No. 834) 2  97-100 NCSK (SEQ. ID. No. 835) 3 237-240 NQSG (SEQ. ID. No. 836) cAMP- and cGMP-dependent protein kinase phosphorylation site 170-173 KRFT (SEQ. ID. No. 837) Protein kinase C phosphorylation site Number of matches: 7 1 89-91 SLK 2 164-166 SSK 3 383-385 SSK 4 169-171 TKR 5 320-322 TFR 6 367-369 SGK 7 164-166 SSK Casein kinase II phosphorylation site Number of matches: 5 1 27-30 SAFD (SEQ. ID. No. 838) 2 75-78 SLLD (SEQ. ID. No. 839) 3 258-261 SGCE (SEQ. ID. No. 840) 4 356-359 SVED (SEQ. ID. No. 841) 5 384-387 SKWE (SEQ. ID. No. 842) N-myristoylation site Number of matches: 6 1 64-69 GAHPTL (SEQ. ID. No. 843) 2 131-136 GGYIAN (SEQ. ID. No. 844) 3 225-230 GVAVNV (SEQ. ID. No. 845) 4 259-264 GCERNH (SEQ. ID. No. 846) 5 287-292 GVLIAA (SEQ. ID. No. 847) 6 402-407 GMYRCT (SEQ. ID. No. 848) Leucine zipper pattern 69-90 LQADDDSLLDQDLPLTNSQLSL (SEQ. ID. No. 849)

TABLE XX Frequently Occurring Motifs avrg. % Name identity Description Potential Function zf-C2H2 34% Zinc finger, C2H2 type Nucleic acid-binding protein functions as transcription factor, nuclear location probable cytochrome_b_N 68% Cytochrome b(N- membrane bound oxidase, generate terminal)/b6/petB superoxide ig 19% Immunoglobulin domain domains are one hundred amino acids long and include a conserved intradomain disulfide bond. WD40 18% WD domain, G-beta repeat tandem repeats of about 40 residues, each containing a Trp-Asp motif. Function in signal transduction and protein interaction PDZ 23% PDZ domain may function in targeting signaling molecules to sub-membranous sites LRR 28% Leucine Rich Repeat short sequence motifs involved in protein- protein interactions pkinase 23% Protein kinase domain conserved catalytic core common to both serine/threonine and tyrosine protein kinases containing an ATP binding site and a catalytic site PH 16% PH domain pleckstrin homology involved in intracellular signaling or as constituents of the cytoskeleton EGF 34% EGF-like domain 30-40 amino-acid long found in the extracellular domain of membrane-bound proteins or in secreted proteins rvt 49% Reverse transcriptase (RNA-dependent DNA polymerase) ank 25% Ank repat Cytoplasmic protein, associates integral membrane proteins to the cytoskeleton oxidored_q1 32% NADH- membrane associated. Involved in proton Ubiquinone/plastoquinone translocation across the membrane complex I), various chains efhand 24% EF hand calcium-binding domain, consists of a12 residue loop flanked on both sides by a 12 residue alpha-helical domain rvp 79% Retroviral aspartyl protease Aspartyl or acid proteases, centered on a catalytic aspartyl residue Collagen 42% Collagen triple helix repeat extracellular structural proteins involved in (20 copies) formation of connective tissue. The sequence consists of the G-X-Y and the polypeptide chains forms a triple helix. fn3 20% Fibronectin type III domain Located in the extracellular ligand-binding region of receptors and is about 200 amino acid residues long with two pairs of cysteines involved in disulfide bonds 7tm_1 19% 7 transmembrane receptor seven hydrophobic transmembrane regions, (rhodopsin family) with the N-terminus located extracellularly while the C-terminus is cytoplasmic. Signal through G proteins

TABLE XXI Properties of 108P5H8 Motifs and localization apply to 108P5H8 variants 1 and 2. Bioinformatic Program Outcome ORF ORF Finder 1290 (includes stop) Protein Length n/a 429 amino acids Transmembrane TM Pred 6 TM, at amino acids region 114-130, 147-163, 181-200, 217-236, 273-295, 306-324 HMMTop 6 TM, at amino acid 113-130, 135-164, 179-202, 215-236, 271-296, 306-331 Sosui 6 TM, at amino acid 113-135, 141-163, 180-202, 215-237, 272-294, 308-330 TMHMM 6 TM, at amino acids 114-136, 146-165, 178-200, 215-237, 273-295, 310-332 Signal Peptide Signal P indicates no signal pI pI/MW tool pI 6.11 Molecular weight pI/MW tool 47.5 kDa Localization PSORT Plasma membrane 60% PSORT II Plasma membrane 43% iPSORT No signal motif Motifs Pfam Ribosomal protein L34; Cation efflux family Prints Rhodopsin Blocks No motif Prosite No motif

TABLE XXII MHC Class 1 nonamer and decamer analysis of 108P5H8 for selected alleles. Listed are scores that fall within the top 50% (rounded up) of all scores for the selected allele. SEQ. ID. Pos 1 2 3 4 5 6 7 8 9 score No. HLA-A*0201 nonamers 278 A L G D L V Q S V 30 1968 121 Y L L F M I G E L 29 1969 153 A I I L T L L A L 28 1970 137 S L A I M T D A L 27 1971  75 S L L D Q D L P L 26 1972 150 D L S A I I L T L 26 1973 268 S L A V R A A F V 26 1974 323 I I W D T V V I I 26 1975 115 T I A A V L Y L L 25 1976 140 I M T D A L H M L 25 1977 181 V L S A M I S V L 25 1978 218 M L I T A A V G V 25 1979 343 Y I K E A L M K I 25 1980 114 L T I A A V L Y L 23 1981 122 L L F M I G E L V 23 1982 146 H M L T D L S A I 23 1983 155 I L T L L A L W L 23 1984 185 M I S V L L V Y I 23 1985 198 L L Y E A V Q R T 23 1986 216 D I M L I T A A V 23 1987 281 D L V Q S V G V L 23 1988 330 I I L E G V P S H 23 1989 331 I L E G V P S H L 23 1990 409 Q L Q S Y R Q E V 23 1991  13 M L R K D D A P L 22 1992  68 T L Q A D D D S L 22 1993 111 K A R L T I A A V 22 1994 133 Y I A N S L A I M 22 1995 183 S A M I S V L L V 22 1996 306 P I C T Y V F S L 22 1997 322 R I I W D T V V I 22 1998 402 G M Y R C T I Q L 22 1999  76 L L D Q D L P L T 21 2000 147 M L T D L S A I I 21 2001 193 I L M G F L L Y E 21 2002 194 L M G F L L Y E A 21 2003 220 I T A A V G V A V 21 2004 349 M K I E D V Y S V 21 2005 118 A V L Y L L F M I 20 2006 124 F M I G E L V G G 20 2007 158 L L A L W L S S K 20 2008 178 R L E V L S A M I 20 2009 212 E I N G D I M L I 20 2010 222 A A V G V A V N V 20 2011 271 V R A A F V H A L 20 2012  80 D L P L T N S Q L 19 2013  82 P L T N S Q L S L 19 2014 104 I L K Q R K V K A 19 2015 143 D A L H M L T D L 19 2016 154 I I L T L L A L W 19 2017 188 V L L V Y I L M G 19 2018 223 A V G V A V N V I 19 2019 302 K I A D P I C T Y 19 2020 327 T V V I I L E G V 19 2021 364 S L T S G K S T A 19 2022 395 H L L L N T F G M 19 2023  41 S R F N K L R V V 18 2024 151 L S A I I L T L L 18 2025 186 I S V L L V Y I L 18 2026 190 L V Y I L M G F L 18 2027 230 V I M G F L L N Q 18 2028 303 I A D P I C T Y V 18 2029 346 E A L M K I E D V 18 2030 365 L T S G K S T A I 18 2031 370 S T A I V H I Q L 18 2032 371 T A I V H I Q L I 18 2033 377 Q L I P G S S S K 18 2034  45 K L R V V V A D D 17 2035  61 P V N G A H P T L 17 2036  87 Q L S L K V D S C 17 2037 184 A M I S V L L V Y 17 2038 205 R T I H M N Y E I 17 2039 219 L I T A A V G V A 17 2040 227 A V N V I M G F L 17 2041 289 L I A A Y I I R F 17 2042 308 C T Y V F S L L V 17 2043 315 L V A F T T F R I 17 2044 357 V E D L N I W S L 17 2045 112 A R L T I A A V L 16 2046 117 A A V L Y L L F M 16 2047 125 M I G E L V G G Y 16 2048 139 A I M T D A L H M 16 2049 148 L T D L S A I I L 16 2050 152 S A I I L T L L A 16 2051 157 T L L A L W L S S 16 2052 174 F G F H R L E V L 16 2053 182 L S A M I S V L L 16 2054 189 L L V Y I L M G F 16 2055 211 Y E I N G D I M L 16 2056 274 A F V H A L G D L 16 2057 275 F V H A L G D L V 16 2058 280 G D L V Q S V G V 16 2059 282 L V Q S V G V L I 16 2060 287 G V L I A A Y I I 16 2061 293 Y I I R F K P E Y 16 2062 313 S L L V A F T T F 16 2063 324 I W D T V V I I L 16 2064 392 K A N H L L L N T 16 2065  5 G A W K R L K S M 15 2066  9 R L K S M L R K D 15 2067  22 F L N D T S A F D 15 2068  27 S A F D F S D E A 15 2069  69 L Q A D D D S L L 15 2070 102 R E I L K Q R K V 15 2071 129 L V G G Y I A N S 15 2072 144 A L H M L T D L S 15 2073 180 E V L S A M I S V 15 2074 192 Y I L M G F L L Y 15 2075 231 I M G F L L N Q S 15 2076 248 S L P S N S P T R 15 2077 295 I R F K P E Y K I 15 2078 310 Y V F S L L V A F 15 2079 314 L L V A F T T F R 15 2080 368 G K S T A I V H I 15 2081 HLA-A*0203 nonamers  49 V V A D D G S E A 12 850  63 N G A H P T L Q A 12 851 110 V K A R L T I A A 12 852  27 S A F D F S D E A 11 853 152 S A I I L T L L A 11 854  57 A P E R P V N G A 10 855 270 A V R A A F V H A 10 856  11 K S M L R K D D A 9 857  20 P L F L N D T S A 9 858  43 F N K L R V V V A 9 859 104 I L K Q R K V K A 9 860 109 K V K A R L T I A 9 861 127 G E L V G G Y I A 9 862 131 G G Y I A N S L A 9 863 136 N S L A I M T D A 9 864 145 L H M L T D L S A 9 865 176 F H R L E V L S A 9 866 194 L M G F L L Y E A 9 867 214 N G D I M L I T A 9 868 215 G D I M L I T A A 9 869 219 L I T A A V G V A 9 870 262 R N H G Q D S L A 9 871 265 G Q D S L A V R A 9 872 266 Q D S L A V R A A 9 873 283 V Q S V G V L I A 9 874 284 Q S V G V L I A A 9 875 296 R F K P E Y K I A 9 876 309 T Y V F S L L V A 9 877 339 L N V D Y I K E A 9 878 364 S L T S G K S T A 9 879 385 K W E E V Q S K A 9 880 414 R Q E V D R T C A 9 881 HLA-A1 nonamers 192 Y I L M G F L L Y 30 882 184 A M I S V L L V Y 25 883 148 L T D L S A I I L 20 884 396 L L L N T F G M Y 20 885  70 Q A D D D S L L D 18 886 113 R L T I A A V L Y 18 887 141 M T D A L H M L T 18 888 347 A L M K I E D V Y 18 889  71 A D D D S L L D Q 17 890 285 S V G V L I A A Y 17 891 293 Y I I R F K P E Y 17 892 324 I W D T V V I I L 17 893 335 V P S H L N V D Y 17 894 356 S V E D L N I W S 17 895 405 R C T I Q L Q S Y 17 896  15 R K D D A P L F L 16 897  31 F S D E A G D E G 16 898 125 M I G E L V G G Y 16 899 203 V Q R T I H M N Y 16 900 302 K I A D P I C T Y 16 901  54 G S E A P E R P V 15 902 HLA-A26 nonamers 310 Y V F S L L V A F 30 903 125 M I G E L V G G Y 28 904 281 D L V Q S V G V L 28 905 285 S V G V L I A A Y 27 906 388 E V Q S K A N H L 27 907 150 D L S A I I L T L 26 908 289 L I A A Y I I R F 26 909 302 K I A D P I C T Y 26 910  80 D L P L T N S Q L 25 911 133 Y I A N S L A I M 25 912 153 A I I L T L L A L 25 913 114 L T I A A V L Y L 24 914 189 L L V Y I L M G F 24 915 192 Y I L M G F L L Y 24 916 293 Y I I R F K P E Y 24 917 115 T I A A V L Y L L 23 918 190 L V Y I L M G F L 23 919 212 E I N G D I M L I 23 920 306 P I C T Y V F S L 23 921 396 L L L N T F G M Y 23 922 168 P T K R F T F G F 22 923 180 E V L S A M I S V 22 924 187 S V L L V Y I L M 22 925 227 A V N V I M G F L 22 926 313 S L L V A F T T F 22 927  61 P V N G A H P T L 21 928 121 Y L L F M I G E L 21 929 128 E L V G G Y I A N 21 930 181 V L S A M I S V L 21 931 326 D T V V I I L E G 21 932  38 E G L S R F N K L 20 933 148 L T D L S A I I L 20 934 331 I L E G V P S H L 20 935 340 N V D Y I K E A L 20 936 370 S T A I V H I Q L 20 937  35 A G D E G L S R F 19 938 113 R L T I A A V L Y 19 939 139 A I M T D A L H M 19 940 171 R F T F G F H R L 19 941 343 Y I K E A L M K I 19 942 347 A L M K I E D V Y 19 943 352 E D V Y S V E D L 19 944 416 E V D R T C A N C 19 945  13 M L R K D D A P L 18 946  21 L F L N D T S A F 18 947  75 S L L D Q D L P L 18 948  82 P L T N S Q L S L 18 949 103 E I L K Q R K V K 18 950 129 L V G G Y I A N S 18 951 137 S L A I M T D A L 18 952 143 D A L H M L T D L 18 953 216 D I M L I T A A V 18 954 267 D S L A V R A A F 18 955 274 A F V H A L G D L 18 956 330 I I L E G V P S H 18 957 399 N T F G M Y R C T 18 958  25 D T S A F D F S D 17 959  68 T L Q A D D D S L 17 960  83 L T N S Q L S L K 17 961 155 I L T L L A L W L 17 962 184 A M I S V L L V Y 17 963 230 V I M G F L L N Q 17 964 353 D V Y S V E D L N 17 965 395 H L L L N T F G M 17 966 405 R C T I Q L Q S Y 17 967  73 D D S L L D Q D L 16 968 116 I A A V L Y L L F 16 969 118 A V L Y L L F M I 16 970 154 I I L T L L A L W 16 971 177 H R L E V L S A M 16 972 185 M I S V L L V Y I 16 973 198 L L Y E A V Q R T 16 974 201 E A V Q R T I H M 16 975 225 G V A V N V I M G 16 976 226 V A V N V I M G F 16 977 229 N V I M G F L L N 16 978 270 A V R A A F V H A 16 979 278 A L G D L V Q S V 16 980 319 T T F R I I W D T 16 981 323 I I W D T V V I I 16 982 334 G V P S H L N V D 16 983 350 K I E D V Y S V E 16 984 378 L I P G S S S K W 16 985  9 R L K S M L R K D 15 986  17 D D A P L F L N D 15 987  76 L L D Q D L P L T 15 988 109 K V K A R L T I A 15 989 158 L L A L W L S S K 15 990 202 A V Q R T I H M N 15 991 261 E R N H G Q D S L 15 992 327 T V V I I L E G V 15 993 373 I V H I Q L I P G 15 994 393 A N H L L L N T F 15 995 406 C T I Q L Q S Y R 15 996 HLA-A3 nonamers 377 Q L I P G S S S K 35 997 113 R L T I A A V L Y 28 998 158 L L A L W L S S K 27 999 197 F L L Y E A V Q R 26 1000 103 E I L K Q R K V K 25 1001 162 W L S S K S P T K 25 1002 294 I I R F K P E Y K 25 1003 302 K I A D P I C T Y 23 1004 322 R I I W D T V V I 23 1005 347 A L M K I E D V Y 23 1006 270 A V R A A F V H A 22 1007 313 S L L V A F T T F 22 1008 192 Y I L M G F L L Y 21 1009 285 S V G V L I A A Y 21 1010 330 I I L E G V P S H 21 1011 361 N I W S L T S G K 21 1012 396 L L L N T F G M Y 21 1013  45 K L R V V V A D D 20 1014 155 I L T L L A L W L 20 1015 184 A M I S V L L V Y 20 1016 218 M L I T A A V G V 20 1017 268 S L A V R A A F V 20 1018 293 Y I I R F K P E Y 20 1019 342 D Y I K E A L M K 20 1020 350 K I E D V Y S V E 20 1021 364 S L T S G K S T A 20 1022 104 I L K Q R K V K A 19 1023 109 K V K A R L T I A 19 1024 150 D L S A I I L T L 19 1025 153 A I I L T L L A L 19 1026 157 T L L A L W L S S 19 1027 181 V L S A M I S V L 19 1028 248 S L P S N S P T R 19 1029 288 V L I A A Y I I R 19 1030 310 Y V F S L L V A F 19 1031 328 V V I I L E G V P 19 1032 329 V I I L E G V P S 19 1033 331 I L E G V P S H L 19 1034  8 K R L K S M L R K 18 1035  49 V V A D D G S E A 18 1036 178 R L E V L S A M I 18 1037 229 N V I M G F L L N 18 1038 234 F L L N Q S G H R 18 1039 282 L V Q S V G V L I 18 1040 359 D L N I W S L T S 18 1041 397 L L N T F G M Y R 18 1042  39 G L S R F N K L R 17 1043  75 S L L D Q D L P L 17 1044  80 D L P L T N S Q L 17 1045 139 A I M T D A L H M 17 1046 193 I L M G F L L Y E 17 1047 202 A V Q R T I H M N 17 1048 223 A V G V A V N V I 17 1049 235 L L N Q S G H R H 17 1050 314 L L V A F T T F R 17 1051 411 Q S Y R Q E V D R 17 1052 HLA-B*0702 nonamers 57 A P E R P V N G A 22 1053  60 R P V N G A H P T 18 1054  2 A G S G A W K R L 16 1055  13 M L R K D D A P L 15 1056  15 R K D D A P L F L 15 1057 106 K Q R K V K A R L 15 1058 150 D L S A I I L T L 15 1059 153 A I I L T L L A L 15 1060  97 N C S K Q R E I L 14 1061 112 A R L T I A A V L 14 1062 114 L T I A A V L Y L 14 1063 167 S P T K R F T F G 14 1064 181 V L S A M I S V L 14 1065 270 A V R A A F V H A 14 1066 271 V R A A F V H A L 14 1067 335 V P S H L N V D Y 14 1068  61 P V N G A H P T L 13 1069  63 N G A H P T L Q A 13 1070  75 S L L D Q D L P L 13 1071 137 S L A I M T D A L 13 1072 155 I L T L L A L W L 13 1073 182 L S A M I S V L L 13 1074 220 I T A A V G V A V 13 1075 227 A V N V I M G F L 13 1076 249 L P S N S P T R G 13 1077 305 D P I C T Y V F S 13 1078 324 I W D T V V I I L 13 1079 331 I L E G V P S H L 13 1080 389 V Q S K A N H L L 13 1081 390 Q S K A N H L L L 13 1082  6 A W K R L K S M L 12 1083  19 A P L F L N D T S 12 1084  38 E G L S R F N K L 12 1085  42 R F N K L R V V V 12 1086  73 D D S L L D Q D L 12 1087  82 P L T N S Q L S L 12 1088 115 T I A A V L Y L L 12 1089 151 L S A I I L T L L 12 1090 171 R F T F G F H R L 12 1091 186 I S V L L V Y I L 12 1092 222 A A V G V A V N V 12 1093 274 A F V H A L G D L 12 1094 281 D L V Q S V G V L 12 1095 298 K P E Y K I A D P 12 1096 307 I C T Y V F S L L 12 1097 340 N V D Y I K E A L 12 1098 352 E D V Y S V E D L 12 1099 365 L T S G K S T A I 12 1100 379 I P G S S S K W E 12 1101  32 S D E A G D E G L 11 1102  54 G S E A P E R P V 11 1103  68 T L Q A D D D S L 11 1104  69 L Q A D D D S L L 11 1105 108 R K V K A R L T I 11 1106 111 K A R L T I A A V 11 1107 117 A A V L Y L L F M 11 1108 130 V G G Y I A N S L 11 1109 139 A I M T D A L H M 11 1110 140 I M T D A L H M L 11 1111 143 D A L H M L T D L 11 1112 148 L T D L S A I I L 11 1113 174 F G F H R L E V L 11 1114 176 F H R L E V L S A 11 1115 190 L V Y I L M G F L 11 1116 191 V Y I L M G F L L 11 1117 223 A V G V A V N V I 11 1118 228 V N V I M G F L L 11 1119 261 E R N H G Q D S L 11 1120 283 V Q S V G V L I A 11 1121 295 I R F K P E Y K I 11 1122 306 P I C T Y V F S L 11 1123 311 V F S L L V A F T 11 1124 322 R I I W D T V V I 11 1125 357 V E D L N I W S L 11 1126 370 S T A I V H I Q L 11 1127 388 E V Q S K A N H L 11 1128 402 G M Y R C T I Q L 11 1129 HLA-B*08 nonamers 104 I L K Q R K V K A 26 1130  13 M L R K D D A P L 22 1131  43 F N K L R V V V A 22 1132 343 Y I K E A L M K I 22 1133 388 E V Q S K A N H L 22 1134 107 Q R K V K A R L T 21 1135 294 I I R F K P E Y K 21 1136  6 A W K R L K S M L 20 1137  38 E G L S R F N K L 20 1138 390 Q S K A N H L L L 20 1139  89 S L K V D S C D N 19 1140 137 S L A I M T D A L 19 1141 164 S S K S P T K R F 19 1142 174 F G F H R L E V L 19 1143  75 S L L D Q D L P L 18 1144  80 D L P L T N S Q L 18 1145  87 Q L S L K V D S C 18 1146  98 C S K Q R E I L K 18 1147 109 K V K A R L T I A 18 1148 121 Y L L F M I G E L 18 1149 155 I L T L L A L W L 18 1150 181 V L S A M I S V L 18 1151 298 K P E Y K I A D P 18 1152  7 W K R L K S M L R 17 1153  56 E A P E R P V N G 17 1154  96 D N C S K Q R E I 17 1155 150 D L S A I I L T L 17 1156 268 S L A V R A A F V 17 1157 281 D L V Q S V G V L 17 1158 331 I L E G V P S H L 17 1159 346 E A L M K I E D V 17 1160 365 L T S G K S T A I 17 1161  9 R L K S M L R K D 16 1162  14 L R K D D A P L F 16 1163  68 T L Q A D D D S L 16 1164  82 P L T N S Q L S L 16 1165 106 K Q R K V K A R L 16 1166 153 A I I L T L L A L 16 1167 162 W L S S K S P T K 16 1168 166 K S P T K R F T F 16 1169 167 S P T K R F T F G 16 1170 168 P T K R F T F G F 16 1171 306 P I C T Y V F S L 15 1172 313 S L L V A F T T F 15 1173  5 G A W K R L K S M 14 1174  45 K L R V V V A D D 14 1175 115 T I A A V L Y L L 14 1176 143 D A L H M L T D L 14 1177 201 E A V Q R T I H M 14 1178 352 E D V Y S V E D L 14 1179  12 S M L R K D D A P 13 1180 105 L K Q R K V K A R 13 1181 111 K A R L T I A A V 13 1182 178 R L E V L S A M I 13 1183 186 I S V L L V Y I L 13 1184 189 L L V Y I L M G F 13 1185 212 E I N G D I M L I 13 1186 258 S G C E R N H G Q 13 1187 271 V R A A F V H A L 13 1188 323 I I W D T V V I I 13 1189 357 V E D L N I W S L 13 1190 383 S S K W E E V Q S 13 1191 HLA-B*1510 nonamers 331 I L E G V P S H L 15 1192  2 A G S G A W K R L 14 1193 106 K Q R K V K A R L 14 1194 181 V L S A M I S V L 14 1195 276 V H A L G D L V Q 14 1196 281 D L V Q S V G V L 14 1197  61 P V N G A H P T L 13 1198  97 N C S K Q R E I L 13 1199 121 Y L L F M I G E L 13 1200 140 I M T D A L H M L 13 1201 150 D L S A I I L T L 13 1202 171 R F T F G F H R L 13 1203 182 L S A M I S V L L 13 1204 186 I S V L L V Y I L 13 1205 271 V R A A F V H A L 13 1206 324 I W D T V V I I L 13 1207 374 V H I Q L I P G S 13 1208  15 R K D D A P L F L 12 1209  32 S D E A G D E G L 12 1210  69 L Q A D D D S L L 12 1211 112 A R L T I A A V L 12 1212 115 T I A A V L Y L L 12 1213 137 S L A I M T D A L 12 1214 155 I L T L L A L W L 12 1215 174 F G F H R L E V L 12 1216 207 I H M N Y E I N G 12 1217 211 Y E I N G D I M L 12 1218 227 A V N V I M G F L 12 1219 244 S H S H S L P S N 12 1220 246 S H S L P S N S P 12 1221 261 E R N H G Q D S L 12 1222 263 N H G Q D S L A V 12 1223 307 I C T Y V F S L L 12 1224 340 N V D Y I K E A L 12 1225 352 E D V Y S V E D L 12 1226 357 V E D L N I W S L 12 1227 389 V Q S K A N H L L 12 1228  6 A W K R L K S M L 11 1229  13 M L R K D D A P L 11 1230  38 E G L S R F N K L 11 1231  68 T L Q A D D D S L 11 1232  73 D D S L L D Q D L 11 1233  75 S L L D Q D L P L 11 1234 114 L T I A A V L Y L 11 1235 151 L S A I I L T L L 11 1236 153 A I I L T L L A L 11 1237 176 F H R L E V L S A 11 1238 190 L V Y I L M G F L 11 1239 240 G H R H S H S H S 11 1240 242 R H S H S H S L P 11 1241 306 P I C T Y V F S L 11 1242 370 S T A I V H I Q L 11 1243 388 E V Q S K A N H L 11 1244 390 Q S K A N H L L L 11 1245 402 G M Y R C T I Q L 11 1246  35 A G D E G L S R F 10 1247  65 A H P T L Q A D D 10 1248  80 D L P L T N S Q L 10 1249  82 P L T N S Q L S L 10 1250 116 I A A V L Y L L F 10 1251 130 V G G Y I A N S L 10 1252 143 D A L H M L T D L 10 1253 145 L H M L T D L S A 10 1254 148 L T D L S A I I L 10 1255 191 V Y I L M G F L L 10 1256 228 V N V I M G F L L 10 1257 241 H R H S H S H S L 10 1258 274 A F V H A L G D L 10 1259 289 L I A A Y I I R F 10 1260 310 Y V F S L L V A F 10 1261 337 S H L N V D Y I K 10 1262 394 N H L L L N T F G 10 1263 164 S S K S P T K R F 9 1264  5 G A W K R L K S M 8 1265  14 L R K D D A P L F 8 1266 133 Y I A N S L A I M 8 1267 166 K S P T K R F T F 8 1268 177 H R L E V L S A M 8 1269 201 E A V Q R T I H M 8 1270 210 N Y E I N G D I M 8 1271 224 V G V A V N V I M 8 1272 267 D S L A V R A A F 8 1273 304 A D P I C T Y V F 8 1274 313 S L L V A F T T F 8 1275  21 L F L N D T S A F 7 1276  55 S E A P E R P V N 7 1277 221 T A A V G V A V N 7 1278 226 V A V N V I M G F 7 1279 393 A N H L L L N T F 7 1280 395 H L L L N T F G M 7 1281 HLA-B*2705 nonamers  8 K R L K S M L R K 30 1282 112 A R L T I A A V L 27 1283 295 I R F K P E Y K I 26 1284 170 K R F T F G F H R 25 1285 261 E R N H G Q D S L 25 1286 101 Q R E I L K Q R K 24 1287 177 H R L E V L S A M 24 1288  14 L R K D D A P L F 22 1289 241 H R H S H S H S L 22 1290 271 V R A A F V H A L 21 1291 106 K Q R K V K A R L 19 1292  35 A G D E G L S R F 18 1293 171 R F T F G F H R L 18 1294 377 Q L I P G S S S K 18 1295 406 C T I Q L Q S Y R 18 1296 163 L S S K S P T K R 17 1297 233 G F L L N Q S G H 17 1298 330 I I L E G V P S H 17 1299 342 D Y I K E A L M K 17 1300 402 G M Y R C T I Q L 17 1301  1 M A G S G A W K R 16 1302  41 S R F N K L R V V 16 1303 100 K Q R E I L K Q R 16 1304 121 Y L L F M I G E L 16 1305 150 D L S A I I L T L 16 1306 153 A I I L T L L A L 16 1307 186 I S V L L V Y I L 16 1308 197 F L L Y E A V Q R 16 1309 211 Y E I N G D I M L 16 1310 226 V A V N V I M G F 16 1311 256 R G S G C E R N H 16 1312 281 D L V Q S V G V L 16 1313 289 L I A A Y I I R F 16 1314 310 Y V F S L L V A F 16 1315 321 F R I I W D T V V 16 1316 357 V E D L N I W S L 16 1317 387 E E V Q S K A N H 16 1318 393 A N H L L L N T F 16 1319  2 A G S G A W K R L 15 1320  5 G A W K R L K S M 15 1321  15 R K D D A P L F L 15 1322  38 E G L S R F N K L 15 1323  82 P L T N S Q L S L 15 1324 103 E I L K Q R K V K 15 1325 108 R K V K A R L T I 15 1326 143 D A L H M L T D L 15 1327 155 I L T L L A L W L 15 1328 174 F G F H R L E V L 15 1329 181 V L S A M I S V L 15 1330 184 A M I S V L L V Y 15 1331 205 R T I H M N Y E I 15 1332 290 I A A Y I I R F K 15 1333 302 K I A D P I C T Y 15 1334 313 S L L V A F T T F 15 1335 331 I L E G V P S H L 15 1336 337 S H L N V D Y I K 15 1337 404 Y R C T I Q L Q S 15 1338 HLA-B*2709 nonamers 112 A R L T I A A V L 25 1339 295 I R F K P E Y K I 22 1340  14 L R K D D A P L F 21 1341 241 H R H S H S H S L 21 1342 271 V R A A F V H A L 21 1343  41 S R F N K L R V V 20 1344 177 H R L E V L S A M 20 1345 261 E R N H G Q D S L 20 1346 321 F R I I W D T V V 19 1347  8 K R L K S M L R K 16 1348 171 R F T F G F H R L 16 1349 402 G M Y R C T I Q L 16 1350  15 R K D D A P L F L 15 1351 287 G V L I A A Y I I 15 1352 322 R I I W D T V V I 15 1353 108 R K V K A R L T I 14 1354 155 I L T L L A L W L 14 1355 170 K R F T F G F H R 14 1356 186 I S V L L V Y I L 14 1357 205 R T I H M N Y E I 14 1358 280 G D L V Q S V G V 14 1359  38 E G L S R F N K L 13 1360  42 R F N K L R V V V 13 1361  75 S L L D Q D L P L 13 1362 102 R E I L K Q R K V 13 1363 106 K Q R K V K A R L 13 1364 114 L T I A A V L Y L 13 1365 132 G Y I A N S L A I 13 1366 153 A I I L T L L A L 13 1367 222 A A V G V A V N V 13 1368 404 Y R C T I Q L Q S 13 1369  2 A G S G A W K R L 12 1370  46 L R V V V A D D G 12 1371  82 P L T N S Q L S L 12 1372 121 Y L L F M I G E L 12 1373 130 V G G Y I A N S L 12 1374 139 A I M T D A L H M 12 1375 140 I M T D A L H M L 12 1376 143 D A L H M L T D L 12 1377 150 D L S A I I L T L 12 1378 174 F G F H R L E V L 12 1379 178 R L E V L S A M I 12 1380 182 L S A M I S V L L 12 1381 190 L V Y I L M G F L 12 1382 227 A V N V I M G F L 12 1383 255 T R G S G C E R N 12 1384 274 A F V H A L G D L 12 1385 281 D L V Q S V G V L 12 1386 299 P E Y K I A D P I 12 1387 307 I C T Y V F S L L 12 1388 310 Y V F S L L V A F 12 1389 324 I W D T V V I I L 12 1390 333 E G V P S H L N V 12 1391 349 M K I E D V Y S V 12 1392 352 E D V Y S V E D L 12 1393 368 G K S T A I V H I 12 1394 381 G S S S K W E E V 12 1395 388 E V Q S K A N H L 12 1396 418 D R T C A N C Q S 12 1397 HLA-B*5101 nonamers 316 V A F T T F R I I 26 1398 143 D A L H M L T D L 25 1399 222 A A V G V A V N V 23 1400 183 S A M I S V L L V 22 1401 346 E A L M K I E D V 22 1402 371 T A I V H I Q L I 22 1403 303 I A D P I C T Y V 21 1404 111 K A R L T I A A V 20 1405 126 I G E L V G G Y I 20 1406  38 E G L S R F N K L 18 1407 174 F G F H R L E V L 18 1408 199 L Y E A V Q R T I 18 1409 209 M N Y E I N G D I 18 1410 286 V G V L I A A Y I 18 1411 323 I I W D T V V I I 18 1412  18 D A P L F L N D T 17 1413 343 Y I K E A L M K I 17 1414  96 D N C S K Q R E I 16 1415 159 L A L W L S S K S 16 1416 195 M G F L L Y E A V 16 1417 221 T A A V G V A V N 16 1418 223 A V G V A V N V I 16 1419 249 L P S N S P T R G 16 1420 269 L A V R A A F V H 16 1421 281 D L V Q S V G V L 16 1422 291 A A Y I I R F K P 16 1423 295 I R F K P E Y K I 16 1424 299 P E Y K I A D P I 16 1425 305 D P I C T Y V F S 16 1426 333 E G V P S H L N V 16 1427  2 A G S G A W K R L 15 1428  19 A P L F L N D T S 15 1429  41 S R F N K L R V V 15 1430  56 E A P E R P V N G 15 1431  81 L P L T N S Q L S 15 1432 130 V G G Y I A N S L 15 1433 150 D L S A I I L T L 15 1434 277 H A L G D L V Q S 15 1435 282 L V Q S V G V L I 15 1436 365 L T S G K S T A I 15 1437  1 M A G S G A W K R 14 1438  5 G A W K R L K S M 14 1439  53 D G S E A P E R P 14 1440 108 R K V K A R L T I 14 1441 134 I A N S L A I M T 14 1442 146 H M L T D L S A I 14 1443 220 I T A A V G V A V 14 1444 226 V A V N V I M G F 14 1445 290 I A A Y I I R F K 14 1446 315 L V A F T T F R I 14 1447 322 R I I W D T V V I 14 1448 324 I W D T V V I I L 14 1449 368 G K S T A I V H I 14 1450 379 I P G S S S K W E 14 1451 400 T F G M Y R C T I 14 1452  42 R F N K L R V V V 13 1453  57 A P E R P V N G A 13 1454  80 D L P L T N S Q L 13 1455 112 A R L T I A A V L 13 1456 116 I A A V L Y L L F 13 1457 117 A A V L Y L L F M 13 1458 118 A V L Y L L F M I 13 1459 138 L A I M T D A L H 13 1460 167 S P T K R F T F G 13 1461 181 V L S A M I S V L 13 1462 185 M I S V L L V Y I 13 1463 273 A A F V H A L G D 13 1464 279 L G D L V Q S V G 13 1465 287 G V L I A A Y I I 13 1466 308 C T Y V F S L L V 13 1467 321 F R I I W D T V V 13 1468 331 I L E G V P S H L 13 1469 335 V P S H L N V D Y 13 1470 349 M K I E D V Y S V 13 1471 SEQ. ID. Pos 1 2 3 4 5 6 7 8 9 0 score No. HLA-A*0201 decamers 139 A I M T D A L H M L 26 1472 184 A M I S V L L V Y I 26 1473 193 I L M G F L L Y E A 26 1474 323 I I W D T V V I I L 26 1475 348 L M K I E D V Y S V 26 1476 198 L L Y E A V Q R T I 25 1477 217 I M L I T A A V G V 25 1478  12 S M L R K D D A P L 24 1479  75 S L L D Q D L P L T 24 1480 113 R L T I A A V L Y L 24 1481 152 S A I I L T L L A L 24 1482 277 H A L G D L V Q S V 24 1483 322 R I I W D T V V I I 24 1484 330 I I L E G V P S H L 24 1485 114 L T I A A V L Y L L 23 1486 121 Y L L F M I G E L V 23 1487 150 D L S A I I L T L L 23 1488 154 I I L T L L A L W L 23 1489 181 V L S A M I S V L L 23 1490 185 M I S V L L V Y I L 23 1491  39 G L S R F N K L R V 22 1492 219 L I T A A V G V A V 22 1493 270 A V R A A F V H A L 22 1494 302 K I A D P I C T Y V 22 1495 356 S V E D L N I W S L 22 1496 129 L V G G Y I A N S L 21 1497 172 F T F G F H R L E V 21 1498 189 L L V Y I L M G F L 21 1499 222 A A V G V A V N V I 21 1500 273 A A F V H A L G D L 21 1501  68 T L Q A D D D S L L 20 1502  83 L T N S Q L S L K V 20 1503 110 V K A R L T I A A V 20 1504 120 L Y L L F M I G E L 20 1505 146 H M L T D L S A I I 20 1506 147 M L T D L S A I I L 20 1507 194 L M G F L L Y E A V 20 1508 197 F L L Y E A V Q R T 20 1509 218 M L I T A A V G V A 20 1510 294 I I R F K P E Y K I 20 1511 314 L L V A F T T F R I 20 1512 338 H L N V D Y I K E A 20 1513 364 S L T S G K S T A I 20 1514 365 L T S G K S T A I V 20 1515 370 S T A I V H I Q L I 20 1516 144 A L H M L T D L S A 19 1517 149 T D L S A I I L T L 19 1518 182 L S A M I S V L L V 19 1519 281 D L V Q S V G V L I 19 1520 117 A A V L Y L L F M I 18 1521 124 F M I G E L V G G Y 18 1522 125 M I G E L V G G Y I 18 1523 153 A I I L T L L A L W 18 1524 157 T L L A L W L S S K 18 1525 188 V L L V Y I L M G F 18 1526 221 T A A V G V A V N V 18 1527 326 D T V V I I L E G V 18 1528 329 V I I L E G V P S H 18 1529  81 L P L T N S Q L S L 17 1530 111 K A R L T I A A V L 17 1531 116 I A A V L Y L L F M 17 1532 160 A L W L S S K S P T 17 1533 180 E V L S A M I S V L 17 1534 190 L V Y I L M G F L L 17 1535 192 Y I L M G F L L Y E 17 1536 227 A V N V I M G F L L 17 1537 230 V I M G F L L N Q S 17 1538 280 G D L V Q S V G V L 17 1539 288 V L I A A Y I I R F 17 1540 305 D P I C T Y V F S L 17 1541 310 Y V F S L L V A F T 17 1542 319 T T F R I I W D T V 17 1543 345 K E A L M K I E D V 17 1544 399 N T F G M Y R C T I 17 1545  5 G A W K R L K S M L 16 1546 133 Y I A N S L A I M T 16 1547 137 S L A I M T D A L H 16 1548 142 T D A L H M L T D L 16 1549 145 L H M L T D L S A I 16 1550 158 L L A L W L S S K S 16 1551 208 H M N Y E I N G D I 16 1552 211 Y E I N G D I M L I 16 1553 215 G D I M L I T A A V 16 1554 285 S V G V L I A A Y I 16 1555 289 L I A A Y I I R F K 16 1556 351 I E D V Y S V E D L 16 1557 359 D L N I W S L T S G 16 1558 377 Q L I P G S S S K W 16 1559 408 I Q L Q S Y R Q E V 16 1560  40 L S R F N K L R V V 15 1561  41 S R F N K L R V V V 15 1562  67 P T L Q A D D D S L 15 1563  76 L L D Q D L P L T N 15 1564 103 E I L K Q R K V K A 15 1565 104 I L K Q R K V K A R 15 1566 128 E L V G G Y I A N S 15 1567 155 I L T L L A L W L S 15 1568 226 V A V N V I M G F L 15 1569 279 L G D L V Q S V G V 15 1570 282 L V Q S V G V L I A 15 1571 306 P I C T Y V F S L L 15 1572 315 L V A F T T F R I I 15 1573 342 D Y I K E A L M K I 15 1574 347 A L M K I E D V Y S 15 1575 367 S G K S T A I V H I 15 1576  31 F S D E A G D E G L 14 1577  79 Q D L P L T N S Q L 14 1578 105 L K Q R K V K A R L 14 1579 122 L L F M I G E L V G 14 1580 140 I M T D A L H M L T 14 1581 148 L T D L S A I I L T 14 1582 177 H R L E V L S A M I 14 1583 179 L E V L S A M I S V 14 1584 220 I T A A V G V A V N 14 1585 234 F L L N Q S G H R H 14 1586 240 G H R H S H S H S L 14 1587 262 R N H G Q D S L A V 14 1588 268 S L A V R A A F V H 14 1589 308 C T Y V F S L L V A 14 1590 313 S L L V A F T T F R 14 1591 331 I L E G V P S H L N 14 1592 339 L N V D Y I K E A L 14 1593 372 A I V H I Q L I P G 14 1594 396 L L L N T F G M Y R 14 1595 397 L L N T F G M Y R C 14 1596 402 G M Y R C T I Q L Q 14 1597  1 M A G S G A W K R L 13 1598  4 S G A W K R L K S M 13 1599  14 L R K D D A P L F L 13 1600  22 F L N D T S A F D F 13 1601  56 E A P E R P V N G A 13 1602  60 R P V N G A H P T L 13 1603 119 V L Y L L F M I G E 13 1604 132 G Y I A N S L A I M 13 1605 134 I A N S L A I M T D 13 1606 136 N S L A I M T D A L 13 1607 138 L A I M T D A L H M 13 1608 170 K R F T F G F H R L 13 1609 173 T F G F H R L E V L 13 1610 187 S V L L V Y I L M G 13 1611 212 E I N G D I M L I T 13 1612 213 I N G D I M L I T A 13 1613 235 L L N Q S G H R H S 13 1614 267 D S L A V R A A F V 13 1615 278 A L G D L V Q S V G 13 1616 321 F R I I W D T V V I 13 1617 332 L E G V P S H L N V 13 1618 335 V P S H L N V D Y I 13 1619 350 K I E D V Y S V E D 13 1620 353 D V Y S V E D L N I 13 1621 391 S K A N H L L L N T 13 1622 392 K A N H L L L N T F 13 1623 HLA-A*0203 decamers 109 K V K A R L T I A A 19 1624 214 N G D I M L I T A A 19 1625 265 G Q D S L A V R A A 19 1626 283 V Q S V G V L I A A 19 1627 110 V K A R L T I A A V 17 1628 215 G D I M L I T A A V 17 1629 266 Q D S L A V R A A F 17 1630 284 Q S V G V L I A A Y 17 1631  10 L K S M L R K D D A 10 1632  19 A P L F L N D T S A 10 1633  26 T S A F D F S D E A 10 1634  42 R F N K L R V V V A 10 1635  48 V V V A D D G S E A 10 1636  56 E A P E R P V N G A 10 1637  62 V N G A H P T L Q A 10 1638 103 E I L K Q R K V K A 10 1639 108 R K V K A R L T I A 10 1640 126 I G E L V G G Y I A 10 1641 130 V G G Y I A N S L A 10 1642 135 A N S L A I M T D A 10 1643 144 A L H M L T D L S A 10 1644 151 L S A I I L T L L A 10 1645 175 G F H R L E V L S A 10 1646 193 I L M G F L L Y E A 10 1647 213 I N G D I M L I T A 10 1648 218 M L I T A A V G V A 10 1649 261 E R N H G Q D S L A 10 1650 264 H G Q D S L A V R A 10 1651 269 L A V R A A F V H A 10 1652 282 L V Q S V G V L I A 10 1653 295 I R F K P E Y K I A 10 1654 308 C T Y V F S L L V A 10 1655 338 H L N V D Y I K E A 10 1656 363 W S L T S G K S T A 10 1657 384 S K W E E V Q S K A 10 1658 413 Y R Q E V D R T C A 10 1659  11 K S M L R K D D A P 9 1660  20 P L F L N D T S A F 9 1661  27 S A F D F S D E A G 9 1662  43 F N K L R V V V A D 9 1663  49 V V A D D G S E A P 9 1664  57 A P E R P V N G A H 9 1665  63 N G A H P T L Q A D 9 1666 104 I L K Q R K V K A R 9 1667 127 G E L V G G Y I A N 9 1668 131 G G Y I A N S L A I 9 1669 136 N S L A I M T D A L 9 1670 145 L H M L T D L S A I 9 1671 152 S A I I L T L L A L 9 1672 176 F H R L E V L S A M 9 1673 194 L M G F L L Y E A V 9 1674 219 L I T A A V G V A V 9 1675 262 R N H G Q D S L A V 9 1676 270 A V R A A F V H A L 9 1677 296 R F K P E Y K I A D 9 1678 309 T Y V F S L L V A F 9 1679 339 L N V D Y I K E A L 9 1680 364 S L T S G K S T A I 9 1681 385 K W E E V Q S K A N 9 1682 414 R Q E V D R T C A N 9 1683 HLA-A1 decamers 191 V Y I L M G F L L Y 27 1684 183 S A M I S V L L V Y 24 1685 141 M T D A L H M L T D 22 1686 148 L T D L S A I I L T 22 1687 284 Q S V G V L I A A Y 20 1688 395 H L L L N T F G M Y 20 1689  16 K D D A P L F L N D 19 1690 112 A R L T I A A V L Y 18 1691 124 F M I G E L V G G Y 18 1692  76 L L D Q D L P L T N 17 1693 301 Y K I A D P I C T Y 17 1694 404 Y R C T I Q L Q S Y 17 1695  54 G S E A P E R P V N 16 1696  70 Q A D D D S L L D Q 16 1697 202 A V Q R T I H M N Y 16 1698 292 A Y I I R F K P E Y 16 1699 324 I W D T V V I I L E 16 1700 334 G V P S H L N V D Y 16 1701 346 E A L M K I E D V Y 16 1702  31 F S D E A G D E G L 15 1703 172 F T F G F H R L E V 15 1704 210 N Y E I N G D I M L 15 1705 303 I A D P I C T Y V F 15 1706  32 S D E A G D E G L S 14 1707  83 L T N S Q L S L K V 14 1708 331 I L E G V P S H L N 14 1709 344 I K E A L M K I E D 14 1710  3 G S G A W K R L K S 13 1711  23 L N D T S A F D F S 13 1712 182 L S A M I S V L L V 13 1713 308 C T Y V F S L L V A 13 1714 357 V E D L N I W S L T 13 1715 HLA-A26 decamers 180 E V L S A M I S V L 30 1716 225 G V A V N V I M G F 27 1717 150 D L S A I I L T L L 26 1718 115 T I A A V L Y L L F 25 1719 288 V L I A A Y I I R F 25 1720 388 E V Q S K A N H L L 25 1721 114 L T I A A V L Y L L 24 1722 188 V L L V Y I L M G F 24 1723 356 S V E D L N I W S L 24 1724  34 E A G D E G L S R F 23 1725 139 A I M T D A L H M L 23 1726 270 A V R A A F V H A L 23 1727 306 P I C T Y V F S L L 23 1728 323 I I W D T V V I I L 23 1729 334 G V P S H L N V D Y 23 1730 395 H L L L N T F G M Y 23 1731  20 P L F L N D T S A F 22 1732 128 E L V G G Y I A N S 22 1733 185 M I S V L L V Y I L 22 1734 202 A V Q R T I H M N Y 22 1735 212 E I N G D I M L I T 22 1736 330 I I L E G V P S H L 22 1737  25 D T S A F D F S D E 21 1738 129 L V G G Y I A N S L 21 1739 305 D P I C T Y V F S L 21 1740 326 D T V V I I L E G V 21 1741  13 M L R K D D A P L F 20 1742  67 P T L Q A D D D S L 20 1743 113 R L T I A A V L Y L 20 1744 189 L L V Y I L M G F L 20 1745 340 N V D Y I K E A L M 20 1746  22 F L N D T S A F D F 19 1747  37 D E G L S R F N K L 19 1748 103 E I L K Q R K V K A 19 1749 124 F M I G E L V G G Y 19 1750 223 A V G V A V N V I M 19 1751 359 D L N I W S L T S G 19 1752 154 I I L T L L A L W L 18 1753 173 T F G F H R L E V L 18 1754 190 L V Y I L M G F L L 18 1755 227 A V N V I M G F L L 18 1756 284 Q S V G V L I A A Y 18 1757 310 Y V F S L L V A F T 18 1758 329 V I I L E G V P S H 18 1759 353 D V Y S V E D L N I 18 1760  68 T L Q A D D D S L L 17 1761  72 D D D S L L D Q D L 17 1762 147 M L T D L S A I I L 17 1763 153 A I I L T L L A L W 17 1764 181 V L S A M I S V L L 17 1765 216 D I M L I T A A V G 17 1766 229 N V I M G F L L N Q 17 1767 230 V I M G F L L N Q S 17 1768 322 R I I W D T V V I I 17 1769 343 Y I K E A L M K I E 17 1770 416 E V D R T C A N C Q 17 1771  80 D L P L T N S Q L S 16 1772 191 V Y I L M G F L L Y 16 1773 205 R T I H M N Y E I N 16 1774 220 I T A A V G V A V N 16 1775 281 D L V Q S V G V L I 16 1776 301 Y K I A D P I C T Y 16 1777 309 T Y V F S L L V A F 16 1778 346 E A L M K I E D V Y 16 1779 370 S T A I V H I Q L I 16 1780 373 I V H I Q L I P G S 16 1781 387 E E V Q S K A N H L 16 1782 404 Y R C T I Q L Q S Y 16 1783  96 D N C S K Q R E I L 15 1784 104 I L K Q R K V K A R 15 1785 118 A V L Y L L F M I G 15 1786 132 G Y I A N S L A I M 15 1787 141 M T D A L H M L T D 15 1788 148 L T D L S A I I L T 15 1789 152 S A I I L T L L A L 15 1790 168 P T K R F T F G F H 15 1791 170 K R F T F G F H R L 15 1792 172 F T F G F H R L E V 15 1793 187 S V L L V Y I L M G 15 1794 193 I L M G F L L Y E A 15 1795 282 L V Q S V G V L I A 15 1796 289 L I A A Y I I R F K 15 1797 315 L V A F T T F R I I 15 1798 342 D Y I K E A L M K I 15 1799 407 T I Q L Q S Y R Q E 15 1800 HLA-A3 decamers 157 T L L A L W L S S K 29 1801  91 K V D S C D N C S K 25 1802 293 Y I I R F K P E Y K 25 1803  82 P L T N S Q L S L K 24 1804 102 R E I L K Q R K V K 23 1805 202 A V Q R T I H M N Y 23 1806 268 S L A V R A A F V H 23 1807 341 V D Y I K E A L M K 22 1808 278 A L G D L V Q S V G 21 1809 289 L I A A Y I I R F K 21 1810 328 V V I I L E G V P S 21 1811 377 Q L I P G S S S K W 21 1812 395 H L L L N T F G M Y 21 1813 396 L L L N T F G M Y R 21 1814  13 M L R K D D A P L F 20 1815 137 S L A I M T D A L H 20 1816 234 F L L N Q S G H R H 20 1817 334 G V P S H L N V D Y 20 1818 376 I Q L I P G S S S K 20 1819  20 P L F L N D T S A F 19 1820  45 K L R V V V A D D G 19 1821 154 I I L T L L A L W L 19 1822 180 E V L S A M I S V L 19 1823 198 L L Y E A V Q R T I 19 1824 216 D I M L I T A A V G 19 1825 270 A V R A A F V H A L 19 1826 275 F V H A L G D L V Q 19 1827 288 V L I A A Y I I R F 19 1828 322 R I I W D T V V I I 19 1829  22 F L N D T S A F D F 18 1830  48 V V V A D D G S E A 18 1831  76 L L D Q D L P L T N 18 1832 104 I L K Q R K V K A R 18 1833 112 A R L T I A A V L Y 18 1834 113 R L T I A A V L Y L 18 1835 115 T I A A V L Y L L F 18 1836 144 A L H M L T D L S A 18 1837 153 A I I L T L L A L W 18 1838 178 R L E V L S A M I S 18 1839 187 S V L L V Y I L M G 18 1840 190 L V Y I L M G F L L 18 1841 218 M L I T A A V G V A 18 1842 219 L I T A A V G V A V 18 1843 313 S L L V A F T T F R 18 1844 329 V I I L E G V P S H 18 1845  7 W K R L K S M L R K 17 1846  47 R V V V A D D G S E 17 1847 100 K Q R E I L K Q R K 17 1848 109 K V K A R L T I A A 17 1849 111 K A R L T I A A V L 17 1850 122 L L F M I G E L V G 17 1851 129 L V G G Y I A N S L 17 1852 160 A L W L S S K S P T 17 1853 188 V L L V Y I L M G F 17 1854 196 G F L L Y E A V Q R 17 1855 223 A V G V A V N V I M 17 1856 281 D L V Q S V G V L I 17 1857 285 S V G V L I A A Y I 17 1858 287 G V L I A A Y I I R 17 1859 330 I I L E G V P S H L 17 1860 347 A L M K I E D V Y S 17 1861 353 D V Y S V E D L N I 17 1862 375 H I Q L I P G S S S 17 1863  9 R L K S M L R K D D 16 1864  39 G L S R F N K L R V 16 1865  87 Q L S L K V D S C D 16 1866 118 A V L Y L L F M I G 16 1867 161 L W L S S K S P T K 16 1868 162 W L S S K S P T K R 16 1869 181 V L S A M I S V L L 16 1870 225 G V A V N V I M G F 16 1871 227 A V N V I M G F L L 16 1872 229 N V I M G F L L N Q 16 1873 327 T V V I I L E G V P 16 1874 350 K I E D V Y S V E D 16 1875 360 L N I W S L T S G K 16 1876 409 Q L Q S Y R Q E V D 16 1877 416 E V D R T C A N C Q 16 1878  2 A G S G A W K R L K 15 1879  33 D E A G D E G L S R 15 1880  68 T L Q A D D D S L L 15 1881 119 V L Y L L F M I G E 15 1882 121 Y L L F M I G E L V 15 1883 128 E L V G G Y I A N S 15 1884 158 L L A L W L S S K S 15 1885 183 S A M I S V L L V Y 15 1886 301 Y K I A D P I C T Y 15 1887  61 P V N G A H P T L Q 14 1888  75 S L L D Q D L P L T 14 1889 103 E I L K Q R K V K A 14 1890 133 Y I A N S L A I M T 14 1891 147 M L T D L S A I I L 14 1892 193 I L M G F L L Y E A 14 1893 284 Q S V G V L I A A Y 14 1894 302 K I A D P I C T Y V 14 1895 331 I L E G V P S H L N 14 1896 356 S V E D L N I W S L 14 1897 359 D L N I W S L T S G 14 1898 383 S S K W E E V Q S K 14 1899 HLA-B*0702 decamers  60 R P V N G A H P T L 22 1900  81 L P L T N S Q L S L 22 1901 305 D P I C T Y V F S L 21 1902  19 A P L F L N D T S A 19 1903 335 V P S H L N V D Y I 19 1904 167 S P T K R F T F G F 18 1905 298 K P E Y K I A D P I 18 1906 270 A V R A A F V H A L 17 1907 111 K A R L T I A A V L 15 1908 181 V L S A M I S V L L 15 1909 389 V Q S K A N H L L L 15 1910 113 R L T I A A V L Y L 14 1911 150 D L S A I I L T L L 14 1912  14 L R K D D A P L F L 13 1913  57 A P E R P V N G A H 13 1914  74 D S L L D Q D L P L 13 1915 129 L V G G Y I A N S L 13 1916 136 N S L A I M T D A L 13 1917 139 A I M T D A L H M L 13 1918 152 S A I I L T L L A L 13 1919 154 I I L T L L A L W L 13 1920 185 M I S V L L V Y I L 13 1921 249 L P S N S P T R G S 13 1922 351 I E D V Y S V E D L 13 1923  12 S M L R K D D A P L 12 1924  37 D E G L S R F N K L 12 1925  42 R F N K L R V V V A 12 1926 142 T D A L H M L T D L 12 1927 149 T D L S A I I L T L 12 1928 170 K R F T F G F H R L 12 1929 173 T F G F H R L E V L 12 1930 180 E V L S A M I S V L 12 1931 222 A A V G V A V N V I 12 1932 227 A V N V I M G F L L 12 1933 240 G H R H S H S H S L 12 1934 260 C E R N H G Q D S L 12 1935 262 R N H G Q D S L A V 12 1936 273 A A F V H A L G D L 12 1937 280 G D L V Q S V G V L 12 1938 323 I I W D T V V I I L 12 1939 365 L T S G K S T A I V 12 1940 369 K S T A I V H I Q L 12 1941 379 I P G S S S K W E E 12 1942 401 F G M Y R C T I Q L 12 1943  1 M A G S G A W K R L 11 1944  5 G A W K R L K S M L 11 1945  31 F S D E A G D E G L 11 1946  62 V N G A H P T L Q A 11 1947  68 T L Q A D D D S L L 11 1948  72 D D D S L L D Q D L 11 1949  79 Q D L P L T N S Q L 11 1950  96 D N C S K Q R E I L 11 1951 105 L K Q R K V K A R L 11 1952 114 L T I A A V L Y L L 11 1953 116 I A A V L Y L L F M 11 1954 135 A N S L A I M T D A 11 1955 172 F T F G F H R L E V 11 1956 189 L L V Y I L M G F L 11 1957 212 E I N G D I M L I T 11 1958 223 A V G V A V N V I M 11 1959 226 V A V N V I M G F L 11 1960 266 Q D S L A V R A A F 11 1961 303 I A D P I C T Y V F 11 1962 306 P I C T Y V F S L L 11 1963 330 I I L E G V P S H L 11 1964 339 L N V D Y I K E A L 11 1965 387 E E V Q S K A N H L 11 1966 388 E V Q S K A N H L L 11 1967 MHC Class 1 nonamer and decamer analysis of 108P5H8 flanking the D to E mutation at amino acid 30. Listed are scores that fall within the top 50% (rounded up) of all scores for a selected allele of the 108P5H8 variant 1 sequence that does not contain the mutation. SEQ. ID. Pos 1 2 3 4 5 6 7 8 9 score No. HLA-A*0201 nonamers  27 S A F E F S D E A 16 2082  22 F L N D T S A F E 15 2083 HLA-A*0203 nonamers  27 S A F E F S D E A 11 2084 HLA-A26 nonamers  25 D T S A F E F S D 17 2085 HLA-B*1510 nonamers  23 L N D T S A F E F 7 2086 HLA-B*5101 decamers  27 S A F E F S D E A 13 2087 SEQ. ID. Pos 1 2 3 4 5 6 7 8 9 0 score No. HLA-A*0201 decamers  22 F L N D T S A F E F 15 2088 HLA-A1 decamers  23 L N D T S A F E F S 13 2089 HLA-A26 decamers  25 D T S A F E F S D E 21 2090  22 F L N D T S A F E F 20 2091 HLA-A3 decamers  22 F L N D T S A F E F 18 2092

TABLE XXIII MHC Class II 15-mer analysis of 108P5H8 for selected alleles. Listed are scores that fall within the top 50% (rounded up) of all scores for the selected allele. SEQ. ID Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 score No. HLA-DRB1*0101 15-mers 326 D T V V I I L E G V P S H L N 36 2093 188 V L L V Y I L M G F L L Y E A 35 2094 145 L H M L T D L S A I I L T L L 33 2095 123 L F M I G E L V G G Y I A N S 32 2096 152 S A I I L T L L A L W L S S K 32 2097 176 F H R L E V L S A M I S V L L 32 2098 283 V Q S V G V L I A A Y I I R F 32 2099 119 V L Y L L F M I G E L V G G Y 31 2100 225 G V A V N V I M G F L L N Q S 31 2101 359 D L N I W S L T S G K S T A I 31 2102 373 I V H I Q L I P G S S S K W E 31 2103 318 F T T F R I I W D T V V I I L 30 2104  40 L S R F N K L R V V V A D D G 29 2105 215 G D I M L I T A A V G V A V N 29 2106  11 K S M L R K D D A P L F L N D 28 2107 179 L E V L S A M I S V L L V Y I 28 2108 173 T F G F H R L E V L S A M I S 27 2109 272 R A A F V H A L G D L V Q S V 27 2110 309 T Y V F S L L V A F T T F R I 27 2111 371 T A I V H I Q L I P G S S S K 27 2112 153 A I I L T L L A L W L S S K S 26 2113 325 W D T V V I I L E G V P S H L 26 2114  4 S G A W K R L K S M L R K D D 25 2115  20 P L F L N D T S A F D F S D E 25 2116  46 L R V V V A D D G S E A P E R 25 2117 101 Q R E I L K Q R K V K A R L T 25 2118 142 T D A L H M L T D L S A I I L 25 2119 192 Y I L M G F L L Y E A V Q R T 25 2120 217 I M L I T A A V G V A V N V I 25 2121 279 L G D L V Q S V G V L I A A Y 25 2122 345 K E A L M K I E D V Y S V E D 25 2123 392 K A N H L L L N T F G M Y R C 25 2124  43 F N K L R V V V A D D G S E A 24 2125  56 E A P E R P V N G A H P T L Q 24 2126 124 F M I G E L V G G Y I A N S L 24 2127 127 G E L V G G Y I A N S L A I M 24 2128 156 L T L L A L W L S S K S P T K 24 2129 183 S A M I S V L L V Y I L M G F 24 2130 284 Q S V G V L I A A Y I I R F K 24 2131 354 V Y S V E D L N I W S L T S G 24 2132 362 I W S L T S G K S T A I V H I 24 2133  18 D A P L F L N D T S A F D F S 23 2134  47 R V V V A D D G S E A P E R P 23 2135  78 D Q D L P L T N S Q L S L K V 23 2136 107 Q R K V K A R L T I A A V L Y 23 2137 148 L T D L S A I I L T L L A L W 23 2138 149 T D L S A I I L T L L A L W L 23 2139 157 T L L A L W L S S K S P T K R 23 2140 187 S V L L V Y I L M G F L L Y E 23 2141 213 I N G D I M L I T A A V G V A 23 2142 214 N G D I M L I T A A V G V A V 23 2143 277 H A L G D L V Q S V G V L I A 23 2144 280 G D L V Q S V G V L I A A Y I 23 2145 312 F S L L V A F T T F R I I W D 23 2146 351 I E D V Y S V E D L N I W S L 23 2147 383 S S K W E E V Q S K A N H L L 23 2148  81 L P L T N S Q L S L K V D S C 22 2149 113 R L T I A A V L Y L L F M I G 22 2150 144 A L H M L T D L S A I I L T L 22 2151 182 L S A M I S V L L V Y I L M G 22 2152 207 I H M N Y E I N G D I M L I T 22 2153 208 H M N Y E I N G D I M L I T A 22 2154 232 M G F L L N Q S G H R H S H S 22 2155 243 H S H S H S L P S N S P T R G 22 2156 265 G Q D S L A V R A A F V H A L 22 2157 328 V V I I L E G V P S H L N V D 22 2158 338 H L N V D Y I K E A L M K I E 22 2159 372 A I V H I Q L I P G S S S K W 22 2160  99 S K Q R E I L K Q R K V K A R 21 2161 305 D P I C T Y V F S L L V A F T 21 2162 340 N V D Y I K E A L M K I E D V 21 2163 111 K A R L T I A A V L Y L L F M 20 2164 134 I A N S L A I M T D A L H M L 20 2165 141 M T D A L H M L T D L S A I I 20 2166 175 G F H R L E V L S A M I S V L 20 2167 194 L M G F L L Y E A V Q R T I H 20 2168 198 L L Y E A V Q R T I H M N Y E 20 2169 260 C E R N H G Q D S L A V R A A 20 2170 292 A Y I I R F K P E Y K I A D P 20 2171 298 K P E Y K I A D P I C T Y V F 20 2172 301 Y K I A D P I C T Y V F S L L 20 2173 307 I C T Y V F S L L V A F T T F 20 2174 329 V I I L E G V P S H L N V D Y 20 2175 346 E A L M K I E D V Y S V E D L 20 2176 348 L M K I E D V Y S V E D L N I 20 2177 356 S V E D L N I W S L T S G K S 20 2178 360 L N I W S L T S G K S T A I V 20 2179 401 F G M Y R C T I Q L Q S Y R Q 20 2180 104 I L K Q R K V K A R L T I A A 19 2181 109 K V K A R L T I A A V L Y L L 19 2182 117 A A V L Y L L F M I G E L V G 19 2183 118 A V L Y L L F M I G E L V G G 19 2184 150 D L S A I I L T L L A L W L S 19 2185 165 S K S P T K R F T F G F H R L 19 2186 171 R F T F G F H R L E V L S A M 19 2187 233 G F L L N Q S G H R H S H S H 19 2188  17 D D A P L F L N D T S A F D F 18 2189  28 A F D F S D E A G D E G L S R 18 2190 130 V G G Y I A N S L A I M T D A 18 2191 184 A M I S V L L V Y I L M G F L 18 2192 186 I S V L L V Y I L M G F L L Y 18 2193 189 L L V Y I L M G F L L Y E A V 18 2194 212 E I N G D I M L I T A A V G V 18 2195 223 A V G V A V N V I M G F L L N 18 2196 268 S L A V R A A F V H A L G D L 18 2197 313 S L L V A F T T F R I I W D T 18 2198 336 P S H L N V D Y I K E A L M K 18 2199 HLA-DRB1*0301 (DR17) 15-mers  11 K S M L R K D D A P L F L N D 30 2200  66 H P T L Q A D D D S L L D Q D 29 2201 137 S L A I M T D A L H M L T D L 28 2202 332 L E G V P S H L N V D Y I K E 27 2203 386 W E E V Q S K A N H L L L N T 26 2204 144 A L H M L T D L S A I I L T L 24 2205  87 Q L S L K V D S C D N C S K Q 23 2206  47 R V V V A D D G S E A P E R P 22 2207  72 D D D S L L D Q D L P L T N S 22 2208  74 D S L L D Q D L P L T N S Q L 22 2209 152 S A I I L T L L A L W L S S K 22 2210 320 T F R I I W D T V V I I L E G 22 2211  10 L K S M L R K D D A P L F L N 21 2212  19 A P L F L N D T S A F D F S D 21 2213  46 L R V V V A D D G S E A P E R 21 2214 113 R L T I A A V L Y L L F M I G 21 2215 178 R L E V L S A M I S V L L V Y 21 2216 210 N Y E I N G D I M L I T A A V 21 2217 328 V V I I L E G V P S H L N V D 21 2218 393 A N H L L L N T F G M Y R C T 21 2219  12 S M L R K D D A P L F L N D T 20 2220  18 D A P L F L N D T S A F D F S 20 2221 101 Q R E I L K Q R K V K A R L T 20 2222 111 K A R L T I A A V L Y L L F M 20 2223 122 L L F M I G E L V G G Y I A N 20 2224 145 L H M L T D L S A I I L T L L 20 2225 179 L E V L S A M I S V L L V Y I 20 2226 186 I S V L L V Y I L M G F L L Y 20 2227 187 S V L L V Y I L M G F L L Y E 20 2228 268 S L A V R A A F V H A L G D L 20 2229 299 P E Y K I A D P I C T Y V F S 20 2230 336 P S H L N V D Y I K E A L M K 20 2231  7 W K R L K S M L R K D D A P L 19 2232  20 P L F L N D T S A F D F S D E 19 2233 120 L Y L L F M I G E L V G G Y I 19 2234 127 G E L V G G Y I A N S L A I M 19 2235 148 L T D L S A I I L T L L A L W 19 2236 183 S A M I S V L L V Y I L M G F 19 2237 188 V L L V Y I L M G F L L Y E A 19 2238 200 Y E A V Q R T I H M N Y E I N 19 2239 225 G V A V N V I M G F L L N Q S 19 2240 286 V G V L I A A Y I I R F K P E 19 2241 292 A Y I I R F K P E Y K I A D P 19 2242 304 A D P I C T Y V F S L L V A F 19 2243 338 H L N V D Y I K E A L M K I E 19 2244 353 D V Y S V E D L N I W S L T S 19 2245  79 Q D L P L T N S Q L S L K V D 18 2246 158 L L A L W L S S K S P T K R F 18 2247 204 Q R T I H M N Y E I N G D I M 18 2248 223 A V G V A V N V I M G F L L N 18 2249 229 N V I M G F L L N Q S G H R H 18 2250 321 F R I I W D T V V I I L E G V 18 2251 325 W D T V V I I L E G V P S H L 18 2252 354 V Y S V E D L N I W S L T S G 18 2253  37 D E G L S R F N K L R V V V A 17 2254  77 L D Q D L P L T N S Q L S L K 17 2255  89 S L K V D S C D N C S K Q R E 17 2256 196 G F L L Y E A V Q R T I H M N 17 2257 221 T A A V G V A V N V I M G F L 17 2258 264 H G Q D S L A V R A A F V H A 17 2259 294 I I R F K P E Y K I A D P I C 17 2260 344 I K E A L M K I E D V Y S V E 17 2261 407 T I Q L Q S Y R Q E V D R T C 17 2262 163 L S S K S P T K R F T F G F H 16 2263 171 R F T F G F H R L E V L S A M 16 2264 206 T I H M N Y E I N G D I M L I 16 2265 258 S G C E R N H G Q D S L A V R 16 2266 276 V H A L G D L V Q S V G V L I 16 2267 337 S H L N V D Y I K E A L M K I 16 2268  3 G S G A W K R L K S M L R K D 15 2269  26 T S A F D F S D E A G D E G L 15 2270  94 S C D N C S K Q R E I L K Q R 15 2271 103 E I L K Q R K V K A R L T I A 15 2272 151 L S A I I L T L L A L W L S S 15 2273 290 I A A Y I I R F K P E Y K I A 15 2274 HLA-DRB1*0401 (DR4Dw4) 15-mers 383 S S K W E E V Q S K A N H L L 28 2275 138 L A I M T D A L H M L T D L S 26 2276 144 A L H M L T D L S A I I L T L 26 2277 196 G F L L Y E A V Q R T I H M N 26 2278 206 T I H M N Y E I N G D I M L I 26 2279 221 T A A V G V A V N V I M G F L 26 2280 312 F S L L V A F T T F R I I W D 26 2281 329 V I I L E G V P S H L N V D Y 26 2282 359 D L N I W S L T S G K S T A I 26 2283  4 S G A W K R L K S M L R K D D 22 2284  19 A P L F L N D T S A F D F S D 22 2285  40 L S R F N K L R V V V A D D G 22 2286 118 A V L Y L L F M I G E L V G G 22 2287 159 L A L W L S S K S P T K R F T 22 2288 173 T F G F H R L E V L S A M I S 22 2289 197 F L L Y E A V Q R T I H M N Y 22 2290 272 R A A F V H A L G D L V Q S V 22 2291 298 K P E Y K I A D P I C T Y V F 22 2292 309 T Y V F S L L V A F T T F R I 22 2293 318 F T T F R I I W D T V V I I L 22 2294 340 N V D Y I K E A L M K I E D V 22 2295 401 F G M Y R C T I Q L Q S Y R Q 22 2296  37 D E G L S R F N K L R V V V A 20 2297  46 L R V V V A D D G S E A P E R 20 2298  47 R V V V A D D G S E A P E R P 20 2299  59 E R P V N G A H P T L Q A D D 20 2300  66 H P T L Q A D D D S L L D Q D 20 2301  74 D S L L D Q D L P L T N S Q L 20 2302  78 D Q D L P L T N S Q L S L K V 20 2303  89 S L K V D S C D N C S K Q R E 20 2304 111 K A R L T I A A V L Y L L F M 20 2305 123 L F M I G E L V G G Y I A N S 20 2306 137 S L A I M T D A L H M L T D L 20 2307 142 T D A L H M L T D L S A I I L 20 2308 145 L H M L T D L S A I I L T L L 20 2309 148 L T D L S A I I L T L L A L W 20 2310 152 S A I I L T L L A L W L S S K 20 2311 153 A I I L T L L A L W L S S K S 20 2312 155 I L T L L A L W L S S K S P T 20 2313 156 L T L L A L W L S S K S P T K 20 2314 176 F H R L E V L S A M I S V L L 20 2315 178 R L E V L S A M I S V L L V Y 20 2316 179 L E V L S A M I S V L L V Y I 20 2317 182 L S A M I S V L L V Y I L M G 20 2318 183 S A M I S V L L V Y I L M G F 20 2319 187 S V L L V Y I L M G F L L Y E 20 2320 188 V L L V Y I L M G F L L Y E A 20 2321 191 V Y I L M G F L L Y E A V Q R 20 2322 192 Y I L M G F L L Y E A V Q R T 20 2323 195 M G F L L Y E A V Q R T I H M 20 2324 210 N Y E I N G D I M L I T A A V 20 2325 216 D I M L I T A A V G V A V N V 20 2326 217 I M L I T A A V G V A V N V I 20 2327 225 G V A V N V I M G F L L N Q S 20 2328 228 V N V I M G F L L N Q S G H R 20 2329 229 N V I M G F L L N Q S G H R H 20 2330 233 G F L L N Q S G H R H S H S H 20 2331 268 S L A V R A A F V H A L G D L 20 2332 273 A A F V H A L G D L V Q S V G 20 2333 276 V H A L G D L V Q S V G V L I 20 2334 280 G D L V Q S V G V L I A A Y I 20 2335 283 V Q S V G V L I A A Y I I R F 20 2336 291 A A Y I I R F K P E Y K I A D 20 2337 308 C T Y V F S L L V A F T T F R 20 2338 311 V F S L L V A F T T F R I I W 20 2339 320 T F R I I W D T V V I I L E G 20 2340 326 D T V V I I L E G V P S H L N 20 2341 336 P S H L N V D Y I K E A L M K 20 2342 338 H L N V D Y I K E A L M K I E 20 2343 345 K E A L M K I E D V Y S V E D 20 2344 346 E A L M K I E D V Y S V E D L 20 2345 348 L M K I E D V Y S V E D L N I 20 2346 351 I E D V Y S V E D L N I W S L 20 2347 354 V Y S V E D L N I W S L T S G 20 2348 362 I W S L T S G K S T A I V H I 20 2349 373 I V H I Q L I P G S S S K W E 20 2350  16 K D D A P L F L N D T S A F D 18 2351  24 N D T S A F D F S D E A G D E 18 2352  34 E A G D E G L S R F N K L R V 18 2353  77 L D Q D L P L T N S Q L S L K 18 2354  86 S Q L S L K V D S C D N C S K 18 2355  99 S K Q R E I L K Q R K V K A R 18 2356 128 E L V G G Y I A N S L A I M T 18 2357 129 L V G G Y I A N S L A I M T D 18 2358 134 I A N S L A I M T D A L H M L 18 2359 149 T D L S A I I L T L L A L W L 18 2360 170 K R F T F G F H R L E V L S A 18 2361 175 G F H R L E V L S A M I S V L 18 2362 213 I N G D I M L I T A A V G V A 18 2363 255 T R G S G C E R N H G Q D S L 18 2364 277 H A L G D L V Q S V G V L I A 18 2365 305 D P I C T Y V F S L L V A F T 18 2366 353 D V Y S V E D L N I W S L T S 18 2367 356 S V E D L N I W S L T S G K S 18 2368 367 S G K S T A I V H I Q L I P G 18 2369 382 S S S K W E E V Q S K A N H L 18 2370 387 E E V Q S K A N H L L L N T F 18 2371 392 K A N H L L L N T F G M Y R C 18 2372 404 Y R C T I Q L Q S Y R Q E V D 18 2373 411 Q S Y R Q E V D R T C A N C Q 18 2374 412 S Y R Q E V D R T C A N C Q S 18 2375  28 A F D F S D E A G D E G L S R 16 2376 130 V G G Y I A N S L A I M T D A 16 2377 169 T K R F T F G F H R L E V L S 16 2378 171 R F T F G F H R L E V L S A M 16 2379 208 H M N Y E I N G D I M L I T A 16 2380 231 I M G F L L N Q S G H R H S H 16 2381 294 I I R F K P E Y K I A D P I C 16 2382 315 L V A F T T F R I I W D T V V 16 2383 322 R I I W D T V V I I L E G V P 16 2384 352 E D V Y S V E D L N I W S L T 16 2385 360 L N I W S L T S G K S T A I V 16 2386 398 L N T F G M Y R C T I Q L Q S 16 2387 410 L Q S Y R Q E V D R T C A N C 16 2388 107 Q R K V K A R L T I A A V L Y 15 2389 386 W E E V Q S K A N H L L L N T 15 2390  7 W K R L K S M L R K D D A P L 14 2391  11 K S M L R K D D A P L F L N D 14 2392  18 D A P L F L N D T S A F D F S 14 2393  43 F N K L R V V V A D D G S E A 14 2394  45 K L R V V V A D D G S E A P E 14 2395  73 D D S L L D Q D L P L T N S Q 14 2396  80 D L P L T N S Q L S L K V D S 14 2397  87 Q L S L K V D S C D N C S K Q 14 2398 101 Q R E I L K Q R K V K A R L T 14 2399 113 R L T I A A V L Y L L F M I G 14 2400 116 I A A V L Y L L F M I G E L V 14 2401 117 A A V L Y L L F M I G E L V G 14 2402 119 V L Y L L F M I G E L V G G Y 14 2403 120 L Y L L F M I G E L V G G Y I 14 2404 122 L L F M I G E L V G G Y I A N 14 2405 126 I G E L V G G Y I A N S L A I 14 2406 127 G E L V G G Y I A N S L A I M 14 2407 131 G G Y I A N S L A I M T D A L 14 2408 158 L L A L W L S S K S P T K R F 14 2409 185 M I S V L L V Y I L M G F L L 14 2410 200 Y E A V Q R T I H M N Y E I N 14 2411 214 N G D I M L I T A A V G V A V 14 2412 215 G D I M L I T A A V G V A V N 14 2413 227 A V N V I M G F L L N Q S G H 14 2414 279 L G D L V Q S V G V L I A A Y 14 2415 285 S V G V L I A A Y I I R F K P 14 2416 286 V G V L I A A Y I I R F K P E 14 2417 287 G V L I A A Y I I R F K P E Y 14 2418 300 E Y K I A D P I C T Y V F S L 14 2419 304 A D P I C T Y V F S L L V A F 14 2420 313 S L L V A F T T F R I I W D T 14 2421 321 F R I I W D T V V I I L E G V 14 2422 325 W D T V V I I L E G V P S H L 14 2423 327 T V V I I L E G V P S H L N V 14 2424 328 V V I I L E G V P S H L N V D 14 2425 332 L E G V P S H L N V D Y I K E 14 2426 341 V D Y I K E A L M K I E D V Y 14 2427 370 S T A I V H I Q L I P G S S S 14 2428 371 T A I V H I Q L I P G S S S K 14 2429 375 H I Q L I P G S S S K W E E V 14 2430 376 I Q L I P G S S S K W E E V Q 14 2431 395 H L L L N T F G M Y R C T I Q 14 2432 400 T F G M Y R C T I Q L Q S Y R 14 2433 407 T I Q L Q S Y R Q E V D R T C 14 2434 414 R Q E V D R T C A N C Q S S S 14 2435 HLA-DRB1*1101 15-mers 197 F L L Y E A V Q R T I H M N Y 25 2436  40 L S R F N K L R V V V A D D G 23 2437 169 T K R F T F G F H R L E V L S 22 2438 173 T F G F H R L E V L S A M I S 22 2439  43 F N K L R V V V A D D G S E A 21 2440 101 Q R E I L K Q R K V K A R L T 21 2441 153 A I I L T L L A L W L S S K S 21 2442 233 G F L L N Q S G H R H S H S H 21 2443 276 V H A L G D L V Q S V G V L I 21 2444 288 V L I A A Y I I R F K P E Y K 21 2445  7 W K R L K S M L R K D D A P L 20 2446  8 K R L K S M L R K D D A P L F 20 2447 120 L Y L L F M I G E L V G G Y I 20 2448 176 F H R L E V L S A M I S V L L 20 2449 411 Q S Y R Q E V D R T C A N C Q 20 2450 116 I A A V L Y L L F M I G E L V 19 2451 214 N G D I M L I T A A V G V A V 19 2452 280 G D L V Q S V G V L I A A Y I 19 2453 322 R I I W D T V V I I L E G V P 19 2454 325 W D T V V I I L E G V P S H L 19 2455 359 D L N I W S L T S G K S T A I 19 2456 142 T D A L H M L T D L S A I I L 18 2457 185 M I S V L L V Y I L M G F L L 18 2458 229 N V I M G F L L N Q S G H R H 18 2459 290 I A A Y I I R F K P E Y K I A 18 2460 294 I I R F K P E Y K I A D P I C 18 2461 309 T Y V F S L L V A F T T F R I 18 2462 326 D T V V I I L E G V P S H L N 18 2463 345 K E A L M K I E D V Y S V E D 18 2464 367 S G K S T A I V H I Q L I P G 18 2465 370 S T A I V H I Q L I P G S S S 18 2466 373 I V H I Q L I P G S S S K W E 18 2467  4 S G A W K R L K S M L R K D D 17 2468 138 L A I M T D A L H M L T D L S 17 2469 189 L L V Y I L M G F L L Y E A V 17 2470 269 L A V R A A F V H A L G D L V 17 2471 318 F T T F R I I W D T V V I I L 17 2472  28 A F D F S D E A G D E G L S R 16 2473  37 D E G L S R F N K L R V V V A 16 2474  98 C S K Q R E I L K Q R K V K A 16 2475 121 Y L L F M I G E L V G G Y I A 16 2476 383 S S K W E E V Q S K A N H L L 16 2477 401 F G M Y R C T I Q L Q S Y R Q 16 2478  1 M A G S G A W K R L K S M L R 15 2479 145 L H M L T D L S A I I L T L L 15 2480 239 S G H R H S H S H S L P S N S 15 2481 323 I I W D T V V I I L E G V P S 15 2482 397 L L N T F G M Y R C T I Q L Q 15 2483  34 E A G D E G L S R F N K L R V 14 2484  83 L T N S Q L S L K V D S C D N 14 2485 123 L F M I G E L V G G Y I A N S 14 2486 158 L L A L W L S S K S P T K R F 14 2487 183 S A M I S V L L V Y I L M G F 14 2488 200 Y E A V Q R T I H M N Y E I N 14 2489 225 G V A V N V I M G F L L N Q S 14 2490 235 L L N Q S G H R H S H S H S L 14 2491 237 N Q S G H R H S H S H S L P S 14 2492 246 S H S L P S N S P T R G S G C 14 2493 248 S L P S N S P T R G S G C E R 14 2494 254 P T R G S G C E R N H G Q D S 14 2495 342 D Y I K E A L M K I E D V Y S 14 2496 361 N I W S L T S G K S T A I V H 14 2497  44 N K L R V V V A D D G S E A P 13 2498  71 A D D D S L L D Q D L P L T N 13 2499  78 D Q D L P L T N S Q L S L K V 13 2500 113 R L T I A A V L Y L L F M I G 13 2501 119 V L Y L L F M I G E L V G G Y 13 2502 124 F M I G E L V G G Y I A N S L 13 2503 128 E L V G G Y I A N S L A I M T 13 2504 135 A N S L A I M T D A L H M L T 13 2505 141 M T D A L H M L T D L S A I I 13 2506 148 L T D L S A I I L T L L A L W 13 2507 149 T D L S A I I L T L L A L W L 13 2508 156 L T L L A L W L S S K S P T K 13 2509 179 L E V L S A M I S V L L V Y I 13 2510 188 V L L V Y I L M G F L L Y E A 13 2511 216 D I M L I T A A V G V A V N V 13 2512 263 N H G Q D S L A V R A A F V H 13 2513 273 A A F V H A L G D L V Q S V G 13 2514 283 V Q S V G V L I A A Y I I R F 13 2515 308 C T Y V F S L L V A F T T F R 13 2516 329 V I I L E G V P S H L N V D Y 13 2517 336 P S H L N V D Y I K E A L M K 13 2518 338 H L N V D Y I K E A L M K I E 13 2519 410 L Q S Y R Q E V D R T C A N C 13 2520  17 D D A P L F L N D T S A F D F 12 2521  46 L R V V V A D D G S E A P E R 12 2522  47 R V V V A D D G S E A P E R P 12 2523  56 E A P E R P V N G A H P T L Q 12 2524  75 S L L D Q D L P L T N S Q L S 12 2525 103 E I L K Q R K V K A R L T I A 12 2526 107 Q R K V K A R L T I A A V L Y 12 2527 117 A A V L Y L L F M I G E L V G 12 2528 126 I G E L V G G Y I A N S L A I 12 2529 152 S A I I L T L L A L W L S S K 12 2530 155 I L T L L A L W L S S K S P T 12 2531 157 T L L A L W L S S K S P T K R 12 2532 182 L S A M I S V L L V Y I L M G 12 2533 187 S V L L V Y I L M G F L L Y E 12 2534 191 V Y I L M G F L L Y E A V Q R 12 2535 192 Y I L M G F L L Y E A V Q R T 12 2536 204 Q R T I H M N Y E I N G D I M 12 2537 211 Y E I N G D I M L I T A A V G 12 2538 212 E I N G D I M L I T A A V G V 12 2539 222 A A V G V A V N V I M G F L L 12 2540 228 V N V I M G F L L N Q S G H R 12 2541 243 H S H S H S L P S N S P T R G 12 2542 315 L V A F T T F R I I W D T V V 12 2543 348 L M K I E D V Y S V E D L N I 12 2544 351 I E D V Y S V E D L N I W S L 12 2545 352 E D V Y S V E D L N I W S L T 12 2546 354 V Y S V E D L N I W S L T S G 12 2547 356 S V E D L N I W S L T S G K S 12 2548 357 V E D L N I W S L T S G K S T 12 2549 371 T A I V H I Q L I P G S S S K 12 2550 372 A I V H I Q L I P G S S S K W 12 2551 391 S K A N H L L L N T F G M Y R 12 2552 MHC class II analysis of 108P5H8 flanking the D to E mutation at amino acid 30. Listed are scores that fall within the top 50% (rounded up) of all scores for a selected allele of the 108P5H8 variant 1 sequence that does not contain the mutation.

SEQ. ID Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 score No. HLA-DRB1*0101 15-mers 20 P L F L N D T S A F E F S D E 25 2553 18 D A P L F L N D T S A F E F S 23 2554 17 D D A P L F L N D T S A F E F 18 2555 28 A F E F S D E A G D E G L S R 18 2556 HLA-DRB1*0301 (DR17) 15-mers 19 A P L F L N D T S A F E F S D 21 2557 18 D A P L F L N D T S A F E F S 20 2558 20 P L F L N D T S A F E F S D E 19 2559 26 T S A F E F S D E A G D E G L 15 2560 HLA-DRB1*0401 (DR4Dw4) 15-mers 19 A P L F L N D T S A F E F S D 22 2561 16 K D D A P L F L N D T S A F E 18 2562 24 N D T S A F E F S D E A G D E 18 2563 28 A F E F S D E A G D E G L S R 16 2564 18 D A P L F L N D T S A F E F S 14 2565 HLA-DRB1*1101 15-mers 28 A F E F S D E A G D E G L S R 16 2566 17 D D A P L F L N D T S A F E F 12 2567 

1. An isolated monoclonal antibody or antibody fragment that specifically binds to a protein having an amino acid sequence of SEQ ID NO:
 2570. 2. The antibody or antibody fragment of claim 1, wherein the monoclonal antibody is recombinantly produced.
 3. The antibody or antibody fragment of claim 1, wherein the antibody or fragment is labeled with a detectable marker.
 4. The antibody or antibody fragment of claim 1, wherein the fragment is selected from the group consisting of Fab, F(ab′)2, Fv and sFv.
 5. The antibody or antibody fragment of claim 1, wherein the antibody is a human antibody, a humanized antibody or a chimeric antibody.
 6. A hybridoma that produces monoclonal antibody that specifically binds to a protein having an amino acid sequence of SEQ ID NO:
 2570. 7. The antibody or antibody fragment of claim 2, wherein the monoclonal antibody is a single chain monoclonal antibody.
 8. The antibody or antibody fragment of claim 1, wherein the antibody or fragment is labeled with an agent.
 9. The antibody or antibody fragment of claim 8, wherein the cytotoxic agent is selected from the group consisting of radioactive isotopes, chemotherapeutic agents and toxins.
 10. The antibody or antibody fragment of claim 9, wherein the radioactive isotope is selected from the group consisting of ²¹¹At, ¹³¹I, ¹²⁵I, ⁹⁰Y, ¹⁸⁶Re, ¹⁸⁸Re, ¹⁵³Sm, ²¹²Bi, ³²P and radioactive isotopes of Lu.
 11. The antibody or antibody fragment of claim 9, wherein the chemotherapeutic agent is selected from the group consisting of taxol, actinomycin, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, gelonin, and calicheamicin.
 12. The antibody or antibody fragment of claim 9, wherein the toxin is selected from the group consisting of diphtheria toxin, enomycin, phenomycin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, mitogellin, modeccin A chain, and alpha-sarcin. 